examples/SummarizeStar/output/SummarizeStar.md
In zhezhangsh/Rnaseq:
title: "Summary of STAR alignment"
author: "Jim Zhang"
date: "2016-03-28"
output:
html_document:
fig_caption: yes
toc: yes
toc_float: true
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
Introduction
This report is a summary of STAR runs on a RNA-seq data set. It uses information provided by the *_Log.final.out file generated from each STAR run.
- Output directory: /home/zhangz/R/source/Rnaseq/examples/SummarizeStar/output
- STAR program: /mnt/isilon/cbmi/variome/rnaseq_workspace/tools/STAR-2.5.1b/bin/Linux_x86_64_static/STAR
- Samtools program: /mnt/isilon/cbmi/variome/bin/Samtools/samtools-1.2/samtools
- Passes: 2
- qsub: TRUE
STAR Parameters:
- runThreadN = 8
- readFilesCommand = zcat
- genomeDir = /mnt/isilon/cbmi/variome/rnaseq_workspace/refs/mm38/star
- sjdbGTFfile = /mnt/isilon/cbmi/variome/rnaseq_workspace/refs/mm38/GCF_000001635.24_GRCm38.p4_genomic.gff
- outSAMtype = SAM
- chimSegmentMin = 32
- outFilterType = BySJout
- outFilterMultimapNmax = 20
- alignSJoverhangMin = 8
- alignSJDBoverhangMin = 1
- outFilterMismatchNmax = 999
- outFilterMismatchNoverLmax = 0.04
- alignIntronMin = 20
- alignIntronMax = 1000000
- alignMatesGapMax = 1000000
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
Summary statistics
| | Min.| 1st Qu.| Median| Mean| 3rd Qu.| Max.|
|:-------------------------------------|-----:|-------:|------:|--------:|-------:|-----:|
|Total input, million reads | 51.71| 55.000| 58.16| 60.06000| 62.0200| 80.45|
|Alignment rate (%), unique mapping | 68.20| 78.450| 79.18| 79.13000| 80.1000| 82.15|
|Alignment rate (%), unique + multiple | 88.22| 93.810| 94.56| 94.47000| 95.4100| 96.13|
|Mismatch rate (%) | 0.16| 0.190| 0.23| 0.22850| 0.2300| 0.48|
|Deletion rate (%) | 0.01| 0.010| 0.01| 0.01075| 0.0100| 0.02|
|Insertion rate (%) | 0.01| 0.010| 0.01| 0.01025| 0.0100| 0.02|
|Too many loci (%) | 0.06| 0.080| 0.14| 0.19400| 0.1800| 2.39|
|Too many mismatch (%) | 0.07| 0.110| 0.15| 0.20700| 0.1725| 2.36|
|Too short (%) | 3.50| 4.215| 4.86| 4.85700| 5.4320| 6.22|
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
Figures
Alignment rate
Total input vs. uniquely aligned, read count
Unique vs. multiple mapping
Unique vs. multiple mapping, percentage
Non-canonical splice sites
Number of non-canonical splice sites identified from each library
Mismatches and INDELs
Percentage of mismatches and INDELs
Outliers
Outlier reads: mapped to too many loci, too many mismatches, too short, and others
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
Tables
Run information
| | Mapping_star | Mapping_end | Speed | Read_length | Number_reads |
|:------------|:---------------:|:---------------:|:-----:|:-----------:|:------------:|
|C2863 | Mar 02 22:41:56 | Mar 02 23:37:16 | 61.96 | 200 | 57,140,539 |
|C2864 | Mar 02 22:37:35 | Mar 02 23:18:57 | 83.66 | 200 | 57,678,077 |
|C2865 | Mar 02 22:39:31 | Mar 02 23:30:15 | 69.19 | 200 | 58,503,755 |
|C2866 | Mar 02 22:39:37 | Mar 02 23:25:53 | 75.39 | 200 | 58,135,820 |
|LPS2867 | Mar 02 22:35:07 | Mar 02 23:18:04 | 77.59 | 200 | 55,539,026 |
|LPS2868 | Mar 02 22:38:00 | Mar 03 06:48:07 | 7.14 | 200 | 58,289,326 |
|LPS2869 | Mar 02 22:38:50 | Mar 02 23:34:38 | 63.05 | 200 | 58,639,284 |
|LPS2870 | Mar 02 22:42:57 | Mar 02 23:27:47 | 72.12 | 200 | 53,890,556 |
|2864C-L1M | Mar 02 22:34:13 | Mar 02 23:25:08 | 69.16 | 200 | 58,689,360 |
|2864C-L2M | Mar 02 22:45:31 | Mar 02 23:48:44 | 76.36 | 200 | 80,451,779 |
|2865C-L2M | Mar 02 22:48:57 | Mar 02 23:44:53 | 77.86 | 200 | 72,586,064 |
|2866C-L1M | Mar 02 22:41:30 | Mar 02 23:21:04 | 83.11 | 200 | 54,809,117 |
|2863C-L1F | Mar 02 22:37:58 | Mar 02 23:29:08 | 84.47 | 200 | 72,036,332 |
|2863C-L2F | Mar 02 22:42:07 | Mar 02 23:38:33 | 68.68 | 200 | 64,598,433 |
|2865C-L1F | Mar 02 22:39:54 | Mar 02 23:31:42 | 70.71 | 200 | 61,046,927 |
|2864C-L3F | Mar 02 22:39:11 | Mar 02 23:30:08 | 61.86 | 200 | 52,533,673 |
|2867LPS-L1M | Mar 02 22:35:00 | Mar 02 23:23:09 | 79.26 | 200 | 63,604,176 |
|2867LPS-L2M | Mar 02 22:38:07 | Mar 02 23:48:53 | 62.72 | 200 | 73,973,748 |
|2868LPS-L2M | Mar 02 22:37:08 | Mar 02 23:32:21 | 66.83 | 200 | 61,501,992 |
|2870LPS-R1M | Mar 02 22:37:12 | Mar 02 23:29:01 | 82.70 | 200 | 71,419,664 |
|2867LPS-R1F | Mar 02 22:38:05 | Mar 02 23:27:38 | 77.52 | 200 | 64,021,829 |
|2870LPS-L1F | Mar 02 22:44:27 | Mar 02 23:46:53 | 69.58 | 200 | 72,399,179 |
|2870LPS-L2F | Mar 02 22:42:38 | Mar 02 23:28:44 | 71.48 | 200 | 54,921,042 |
|2868LPS-R1F | Mar 02 22:37:28 | Mar 02 23:22:14 | 91.67 | 200 | 68,396,671 |
|2864C-L1ML | Mar 02 22:50:13 | Mar 02 23:33:09 | 77.39 | 200 | 55,378,147 |
|2864C-L2ML | Mar 02 22:35:15 | Mar 02 23:22:40 | 74.22 | 200 | 58,653,865 |
|2865C-L2ML | Mar 02 22:43:08 | Mar 02 23:21:02 | 86.34 | 200 | 54,537,485 |
|2866C-L1ML | Mar 02 22:39:19 | Mar 02 23:19:38 | 78.92 | 200 | 53,027,128 |
|2863C-L1FL | Mar 02 22:41:36 | Mar 02 23:26:29 | 77.56 | 200 | 58,022,655 |
|2863C-L2FL | Mar 02 22:39:06 | Mar 02 23:19:47 | 85.57 | 200 | 58,024,246 |
|2865C-L1FL | Mar 02 22:38:24 | Mar 02 23:17:47 | 88.65 | 200 | 58,187,304 |
|2864C-L3FL | Mar 02 22:37:42 | Mar 02 23:14:32 | 84.23 | 200 | 51,709,700 |
|2867LPS-L1ML | Mar 02 23:00:57 | Mar 02 23:43:49 | 80.97 | 200 | 57,847,860 |
|2867LPS-L2ML | Mar 02 22:42:27 | Mar 02 23:22:01 | 85.28 | 200 | 56,239,877 |
|2868LPS-L2ML | Mar 02 22:46:53 | Mar 02 23:33:36 | 74.99 | 200 | 58,388,067 |
|2870LPS-R1ML | Mar 02 22:45:28 | Mar 02 23:29:30 | 74.43 | 200 | 54,620,369 |
|2867LPS-R1FL | Mar 02 22:38:29 | Mar 02 23:22:19 | 75.31 | 200 | 55,019,421 |
|2870LPS-L1FL | Mar 02 22:40:10 | Mar 02 23:19:37 | 83.02 | 200 | 54,587,346 |
|2870LPS-L2FL | Mar 02 22:40:11 | Mar 02 23:16:30 | 90.74 | 200 | 54,919,965 |
|2868LPS-R1FL | Mar 02 22:48:19 | Mar 02 23:31:39 | 80.72 | 200 | 58,294,557 |
- Speed: mapping speed, million of reads per hour
Mapping results
Mapped reads, count
| | Input | Unique | Splice | Multiple | Chimeric |
|:------------|:----------:|:----------:|:----------:|:----------:|:---------:|
|C2863 | 57,140,539 | 45,224,859 | 26,333,237 | 8,024,212 | 1,475,089 |
|C2864 | 57,678,077 | 47,383,434 | 25,898,212 | 7,206,858 | 1,256,945 |
|C2865 | 58,503,755 | 47,651,274 | 27,994,992 | 7,820,951 | 1,242,161 |
|C2866 | 58,135,820 | 47,541,874 | 28,218,827 | 7,804,069 | 1,230,573 |
|LPS2867 | 55,539,026 | 43,613,088 | 24,174,654 | 8,430,152 | 1,167,810 |
|LPS2868 | 58,289,326 | 39,750,752 | 20,454,935 | 11,667,973 | 1,088,004 |
|LPS2869 | 58,639,284 | 45,995,298 | 26,013,427 | 9,211,372 | 1,252,805 |
|LPS2870 | 53,890,556 | 42,915,321 | 24,929,460 | 7,858,178 | 1,337,109 |
|2864C-L1M | 58,689,360 | 47,001,317 | 26,624,387 | 7,846,028 | 1,272,954 |
|2864C-L2M | 80,451,779 | 63,405,469 | 42,143,077 | 11,812,014 | 1,667,531 |
|2865C-L2M | 72,586,064 | 57,553,609 | 34,476,997 | 10,537,528 | 1,435,442 |
|2866C-L1M | 54,809,117 | 42,934,584 | 24,748,780 | 8,284,712 | 1,332,597 |
|2863C-L1F | 72,036,332 | 58,001,207 | 33,989,766 | 10,017,133 | 1,196,370 |
|2863C-L2F | 64,598,433 | 51,268,448 | 30,829,437 | 9,443,038 | 1,296,505 |
|2865C-L1F | 61,046,927 | 47,967,935 | 29,086,955 | 9,163,766 | 1,220,950 |
|2864C-L3F | 52,533,673 | 41,102,200 | 25,438,748 | 7,940,453 | 984,329 |
|2867LPS-L1M | 63,604,176 | 49,899,708 | 30,505,878 | 9,933,706 | 1,172,921 |
|2867LPS-L2M | 73,973,748 | 58,458,707 | 33,813,429 | 10,802,547 | 1,201,700 |
|2868LPS-L2M | 61,501,992 | 48,488,801 | 30,440,441 | 9,205,426 | 1,120,997 |
|2870LPS-R1M | 71,419,664 | 56,415,555 | 34,407,365 | 10,795,087 | 1,217,153 |
|2867LPS-R1F | 64,021,829 | 50,953,706 | 31,429,140 | 9,503,196 | 1,145,599 |
|2870LPS-L1F | 72,399,179 | 57,362,319 | 33,803,580 | 11,048,257 | 1,406,930 |
|2870LPS-L2F | 54,921,042 | 43,207,998 | 25,008,930 | 8,579,499 | 1,078,581 |
|2868LPS-R1F | 68,396,671 | 55,481,671 | 32,971,296 | 9,589,405 | 1,117,870 |
|2864C-L1ML | 55,378,147 | 44,377,346 | 27,240,083 | 8,670,199 | 618,787 |
|2864C-L2ML | 58,653,865 | 47,972,002 | 26,608,206 | 8,293,513 | 722,236 |
|2865C-L2ML | 54,537,485 | 43,733,356 | 26,619,177 | 8,480,904 | 727,812 |
|2866C-L1ML | 53,027,128 | 42,320,800 | 25,685,569 | 8,412,377 | 685,823 |
|2863C-L1FL | 58,022,655 | 45,357,738 | 27,277,980 | 10,040,391 | 718,124 |
|2863C-L2FL | 58,024,246 | 45,510,473 | 26,615,352 | 9,898,771 | 902,847 |
|2865C-L1FL | 58,187,304 | 47,532,703 | 27,206,258 | 8,402,650 | 736,612 |
|2864C-L3FL | 51,709,700 | 41,603,095 | 26,594,377 | 7,782,242 | 637,614 |
|2867LPS-L1ML | 57,847,860 | 45,148,732 | 26,624,813 | 9,790,283 | 875,730 |
|2867LPS-L2ML | 56,239,877 | 44,303,899 | 22,323,854 | 9,119,871 | 748,474 |
|2868LPS-L2ML | 58,388,067 | 45,258,906 | 26,402,812 | 10,581,691 | 766,297 |
|2870LPS-R1ML | 54,620,369 | 42,614,662 | 27,083,959 | 9,320,797 | 719,779 |
|2867LPS-R1FL | 55,019,421 | 42,322,141 | 25,179,090 | 9,858,585 | 830,127 |
|2870LPS-L1FL | 54,587,346 | 43,244,708 | 25,303,265 | 8,514,727 | 955,917 |
|2870LPS-L2FL | 54,919,965 | 43,882,184 | 25,016,165 | 8,508,797 | 912,717 |
|2868LPS-R1FL | 58,294,557 | 46,395,146 | 27,426,807 | 9,418,469 | 679,156 |
- Unique: reads mapped to one and only one genomic loci
- Splice: reads mapped to splice junctions
- Multiple: reads mapped to multiple genomic loci
Mapped reads, percentage
| | Input | Unique | Splice | Multiple | Chimeric |
|:------------|:-----:|:------:|:------:|:--------:|:--------:|
|C2863 | 100 | 79.15 | 46.09 | 14.04 | 2.58 |
|C2864 | 100 | 82.15 | 44.90 | 12.49 | 2.18 |
|C2865 | 100 | 81.45 | 47.85 | 13.37 | 2.12 |
|C2866 | 100 | 81.78 | 48.54 | 13.42 | 2.12 |
|LPS2867 | 100 | 78.53 | 43.53 | 15.18 | 2.10 |
|LPS2868 | 100 | 68.20 | 35.09 | 20.02 | 1.87 |
|LPS2869 | 100 | 78.44 | 44.36 | 15.71 | 2.14 |
|LPS2870 | 100 | 79.63 | 46.26 | 14.58 | 2.48 |
|2864C-L1M | 100 | 80.08 | 45.36 | 13.37 | 2.17 |
|2864C-L2M | 100 | 78.81 | 52.38 | 14.68 | 2.07 |
|2865C-L2M | 100 | 79.29 | 47.50 | 14.52 | 1.98 |
|2866C-L1M | 100 | 78.33 | 45.15 | 15.12 | 2.43 |
|2863C-L1F | 100 | 80.52 | 47.18 | 13.91 | 1.66 |
|2863C-L2F | 100 | 79.36 | 47.72 | 14.62 | 2.01 |
|2865C-L1F | 100 | 78.58 | 47.65 | 15.01 | 2.00 |
|2864C-L3F | 100 | 78.24 | 48.42 | 15.11 | 1.87 |
|2867LPS-L1M | 100 | 78.45 | 47.96 | 15.62 | 1.84 |
|2867LPS-L2M | 100 | 79.03 | 45.71 | 14.60 | 1.62 |
|2868LPS-L2M | 100 | 78.84 | 49.50 | 14.97 | 1.82 |
|2870LPS-R1M | 100 | 78.99 | 48.18 | 15.12 | 1.70 |
|2867LPS-R1F | 100 | 79.59 | 49.09 | 14.84 | 1.79 |
|2870LPS-L1F | 100 | 79.23 | 46.69 | 15.26 | 1.94 |
|2870LPS-L2F | 100 | 78.67 | 45.54 | 15.62 | 1.96 |
|2868LPS-R1F | 100 | 81.12 | 48.21 | 14.02 | 1.63 |
|2864C-L1ML | 100 | 80.14 | 49.19 | 15.66 | 1.12 |
|2864C-L2ML | 100 | 81.79 | 45.36 | 14.14 | 1.23 |
|2865C-L2ML | 100 | 80.19 | 48.81 | 15.55 | 1.33 |
|2866C-L1ML | 100 | 79.81 | 48.44 | 15.86 | 1.29 |
|2863C-L1FL | 100 | 78.17 | 47.01 | 17.30 | 1.24 |
|2863C-L2FL | 100 | 78.43 | 45.87 | 17.06 | 1.56 |
|2865C-L1FL | 100 | 81.69 | 46.76 | 14.44 | 1.27 |
|2864C-L3FL | 100 | 80.46 | 51.43 | 15.05 | 1.23 |
|2867LPS-L1ML | 100 | 78.05 | 46.03 | 16.92 | 1.51 |
|2867LPS-L2ML | 100 | 78.78 | 39.69 | 16.22 | 1.33 |
|2868LPS-L2ML | 100 | 77.51 | 45.22 | 18.12 | 1.31 |
|2870LPS-R1ML | 100 | 78.02 | 49.59 | 17.06 | 1.32 |
|2867LPS-R1FL | 100 | 76.92 | 45.76 | 17.92 | 1.51 |
|2870LPS-L1FL | 100 | 79.22 | 46.35 | 15.60 | 1.75 |
|2870LPS-L2FL | 100 | 79.90 | 45.55 | 15.49 | 1.66 |
|2868LPS-R1FL | 100 | 79.59 | 47.05 | 16.16 | 1.17 |
Splice sites, count
| | Total | Annotated | GT/AG | GC/AG | AT/AC | Non-canonical |
|:------------|:----------:|:----------:|:----------:|:-------:|:------:|:-------------:|
|C2863 | 26,333,237 | 26,284,251 | 25,963,802 | 314,477 | 18,300 | 36,658 |
|C2864 | 25,898,212 | 25,843,982 | 25,560,618 | 256,138 | 19,278 | 62,178 |
|C2865 | 27,994,992 | 27,942,859 | 27,621,298 | 327,762 | 18,908 | 27,024 |
|C2866 | 28,218,827 | 28,166,516 | 27,833,989 | 337,013 | 19,509 | 28,316 |
|LPS2867 | 24,174,654 | 24,118,600 | 23,813,489 | 290,766 | 16,138 | 54,261 |
|LPS2868 | 20,454,935 | 20,380,706 | 20,126,751 | 209,396 | 12,409 | 106,379 |
|LPS2869 | 26,013,427 | 25,952,955 | 25,621,642 | 321,513 | 16,618 | 53,654 |
|LPS2870 | 24,929,460 | 24,882,986 | 24,593,425 | 271,929 | 17,634 | 46,472 |
|2864C-L1M | 26,624,387 | 26,554,452 | 26,355,231 | 193,107 | 20,454 | 55,595 |
|2864C-L2M | 42,143,077 | 42,056,254 | 41,746,958 | 298,516 | 27,182 | 70,421 |
|2865C-L2M | 34,476,997 | 34,385,277 | 34,121,961 | 258,877 | 26,654 | 69,505 |
|2866C-L1M | 24,748,780 | 24,678,243 | 24,488,648 | 194,770 | 19,920 | 45,442 |
|2863C-L1F | 33,989,766 | 33,902,132 | 33,634,335 | 254,083 | 25,939 | 75,409 |
|2863C-L2F | 30,829,437 | 30,750,920 | 30,506,117 | 226,853 | 22,905 | 73,562 |
|2865C-L1F | 29,086,955 | 29,011,712 | 28,791,467 | 219,071 | 21,595 | 54,822 |
|2864C-L3F | 25,438,748 | 25,374,273 | 25,178,118 | 184,901 | 18,981 | 56,748 |
|2867LPS-L1M | 30,505,878 | 30,417,290 | 30,194,988 | 229,892 | 23,256 | 57,742 |
|2867LPS-L2M | 33,813,429 | 33,718,608 | 33,462,679 | 253,626 | 25,054 | 72,070 |
|2868LPS-L2M | 30,440,441 | 30,365,104 | 30,121,927 | 241,602 | 22,982 | 53,930 |
|2870LPS-R1M | 34,407,365 | 34,312,071 | 34,029,626 | 291,474 | 28,419 | 57,846 |
|2867LPS-R1F | 31,429,140 | 31,345,312 | 31,102,441 | 228,886 | 22,915 | 74,898 |
|2870LPS-L1F | 33,803,580 | 33,713,782 | 33,446,532 | 276,295 | 25,749 | 55,004 |
|2870LPS-L2F | 25,008,930 | 24,939,563 | 24,746,689 | 196,187 | 19,618 | 46,436 |
|2868LPS-R1F | 32,971,296 | 32,889,105 | 32,632,029 | 244,181 | 25,010 | 70,076 |
|2864C-L1ML | 27,240,083 | 27,200,308 | 26,922,227 | 278,731 | 14,352 | 24,773 |
|2864C-L2ML | 26,608,206 | 26,559,204 | 26,285,777 | 278,187 | 15,512 | 28,730 |
|2865C-L2ML | 26,619,177 | 26,576,905 | 26,294,250 | 284,647 | 15,800 | 24,480 |
|2866C-L1ML | 25,685,569 | 25,641,297 | 25,367,178 | 280,744 | 15,891 | 21,756 |
|2863C-L1FL | 27,277,980 | 27,229,163 | 26,934,955 | 301,570 | 17,447 | 24,008 |
|2863C-L2FL | 26,615,352 | 26,570,659 | 26,280,666 | 293,676 | 15,383 | 25,627 |
|2865C-L1FL | 27,206,258 | 27,159,692 | 26,851,620 | 309,506 | 17,758 | 27,374 |
|2864C-L3FL | 26,594,377 | 26,555,264 | 26,295,675 | 261,508 | 14,443 | 22,751 |
|2867LPS-L1ML | 26,624,813 | 26,574,570 | 26,258,828 | 317,746 | 16,665 | 31,574 |
|2867LPS-L2ML | 22,323,854 | 22,273,295 | 22,004,252 | 274,779 | 14,128 | 30,695 |
|2868LPS-L2ML | 26,402,812 | 26,350,260 | 25,993,736 | 363,729 | 18,936 | 26,411 |
|2870LPS-R1ML | 27,083,959 | 27,042,790 | 26,730,101 | 313,681 | 16,707 | 23,470 |
|2867LPS-R1FL | 25,179,090 | 25,130,573 | 24,830,003 | 307,120 | 16,429 | 25,538 |
|2870LPS-L1FL | 25,303,265 | 25,262,204 | 24,994,694 | 264,074 | 15,844 | 28,653 |
|2870LPS-L2FL | 25,016,165 | 24,973,046 | 24,698,575 | 272,901 | 16,536 | 28,153 |
|2868LPS-R1FL | 27,426,807 | 27,378,227 | 27,062,350 | 319,158 | 18,795 | 26,504 |
Mismatches and INDELs
| | Mismatch_rate | Deletion_rate | Insertion_rate | Avg_deletion_length | Avg_insertion_length |
|:------------|:-------------:|:-------------:|:--------------:|:-------------------:|:--------------------:|
|C2863 | 0.20% | 0.01% | 0.01% | 2.06 | 1.97 |
|C2864 | 0.29% | 0.01% | 0.01% | 2.11 | 1.84 |
|C2865 | 0.29% | 0.01% | 0.01% | 2.09 | 1.97 |
|C2866 | 0.28% | 0.01% | 0.01% | 2.05 | 1.80 |
|LPS2867 | 0.33% | 0.02% | 0.02% | 2.20 | 2.39 |
|LPS2868 | 0.48% | 0.02% | 0.01% | 1.92 | 1.94 |
|LPS2869 | 0.31% | 0.01% | 0.01% | 2.12 | 2.17 |
|LPS2870 | 0.30% | 0.01% | 0.01% | 2.13 | 1.93 |
|2864C-L1M | 0.17% | 0.02% | 0.01% | 2.04 | 1.80 |
|2864C-L2M | 0.19% | 0.01% | 0.01% | 2.10 | 1.76 |
|2865C-L2M | 0.18% | 0.01% | 0.01% | 2.16 | 1.77 |
|2866C-L1M | 0.18% | 0.01% | 0.01% | 2.11 | 1.85 |
|2863C-L1F | 0.17% | 0.01% | 0.01% | 2.07 | 1.80 |
|2863C-L2F | 0.18% | 0.01% | 0.01% | 2.08 | 1.83 |
|2865C-L1F | 0.19% | 0.01% | 0.01% | 2.14 | 1.83 |
|2864C-L3F | 0.20% | 0.01% | 0.01% | 2.16 | 2.12 |
|2867LPS-L1M | 0.23% | 0.01% | 0.01% | 2.17 | 1.83 |
|2867LPS-L2M | 0.24% | 0.01% | 0.01% | 2.18 | 2.00 |
|2868LPS-L2M | 0.18% | 0.01% | 0.01% | 2.17 | 1.81 |
|2870LPS-R1M | 0.23% | 0.01% | 0.01% | 2.23 | 1.89 |
|2867LPS-R1F | 0.20% | 0.01% | 0.01% | 2.12 | 1.77 |
|2870LPS-L1F | 0.20% | 0.01% | 0.01% | 2.16 | 1.87 |
|2870LPS-L2F | 0.20% | 0.01% | 0.01% | 2.17 | 2.08 |
|2868LPS-R1F | 0.19% | 0.01% | 0.01% | 2.16 | 1.90 |
|2864C-L1ML | 0.23% | 0.01% | 0.01% | 2.14 | 1.65 |
|2864C-L2ML | 0.23% | 0.01% | 0.01% | 2.13 | 1.68 |
|2865C-L2ML | 0.23% | 0.01% | 0.01% | 2.12 | 1.68 |
|2866C-L1ML | 0.22% | 0.01% | 0.01% | 2.09 | 1.67 |
|2863C-L1FL | 0.23% | 0.01% | 0.01% | 2.08 | 1.68 |
|2863C-L2FL | 0.16% | 0.01% | 0.01% | 2.05 | 1.61 |
|2865C-L1FL | 0.23% | 0.01% | 0.01% | 2.14 | 1.66 |
|2864C-L3FL | 0.23% | 0.01% | 0.01% | 2.14 | 1.65 |
|2867LPS-L1ML | 0.19% | 0.01% | 0.01% | 2.24 | 1.68 |
|2867LPS-L2ML | 0.23% | 0.01% | 0.01% | 2.23 | 1.69 |
|2868LPS-L2ML | 0.19% | 0.01% | 0.01% | 2.18 | 1.70 |
|2870LPS-R1ML | 0.24% | 0.01% | 0.01% | 2.16 | 1.63 |
|2867LPS-R1FL | 0.23% | 0.01% | 0.01% | 2.16 | 1.57 |
|2870LPS-L1FL | 0.23% | 0.01% | 0.01% | 2.07 | 1.61 |
|2870LPS-L2FL | 0.23% | 0.01% | 0.01% | 2.10 | 1.64 |
|2868LPS-R1FL | 0.23% | 0.01% | 0.01% | 2.18 | 1.70 |
- Rates are per base
Outliers
| | Too_many_loci | Too_many_mismatch | Too_short | Other |
|:------------|:-------------:|:-----------------:|:---------:|:-----:|
|C2863 | 0.26% | 0.17% | 6.22% | 0.16% |
|C2864 | 0.20% | 0.18% | 4.78% | 0.19% |
|C2865 | 0.20% | 0.21% | 4.62% | 0.16% |
|C2866 | 0.19% | 0.13% | 4.36% | 0.12% |
|LPS2867 | 0.26% | 0.41% | 5.51% | 0.12% |
|LPS2868 | 2.39% | 2.36% | 5.22% | 1.83% |
|LPS2869 | 0.30% | 0.29% | 5.13% | 0.14% |
|LPS2870 | 0.27% | 0.19% | 5.21% | 0.11% |
|2864C-L1M | 0.18% | 0.15% | 5.73% | 0.49% |
|2864C-L2M | 0.18% | 0.10% | 5.89% | 0.34% |
|2865C-L2M | 0.16% | 0.10% | 5.47% | 0.46% |
|2866C-L1M | 0.14% | 0.11% | 5.96% | 0.34% |
|2863C-L1F | 0.14% | 0.08% | 4.91% | 0.45% |
|2863C-L2F | 0.14% | 0.10% | 5.42% | 0.36% |
|2865C-L1F | 0.13% | 0.12% | 5.87% | 0.30% |
|2864C-L3F | 0.19% | 0.20% | 5.84% | 0.42% |
|2867LPS-L1M | 0.16% | 0.11% | 5.31% | 0.35% |
|2867LPS-L2M | 0.18% | 0.20% | 5.56% | 0.43% |
|2868LPS-L2M | 0.14% | 0.10% | 5.60% | 0.34% |
|2870LPS-R1M | 0.12% | 0.12% | 5.42% | 0.24% |
|2867LPS-R1F | 0.15% | 0.11% | 4.87% | 0.43% |
|2870LPS-L1F | 0.16% | 0.13% | 4.90% | 0.32% |
|2870LPS-L2F | 0.15% | 0.18% | 5.04% | 0.34% |
|2868LPS-R1F | 0.14% | 0.12% | 4.22% | 0.39% |
|2864C-L1ML | 0.07% | 0.15% | 3.85% | 0.14% |
|2864C-L2ML | 0.08% | 0.15% | 3.67% | 0.17% |
|2865C-L2ML | 0.08% | 0.15% | 3.88% | 0.15% |
|2866C-L1ML | 0.07% | 0.14% | 4.02% | 0.10% |
|2863C-L1FL | 0.08% | 0.14% | 4.20% | 0.11% |
|2863C-L2FL | 0.08% | 0.07% | 4.24% | 0.12% |
|2865C-L1FL | 0.08% | 0.15% | 3.50% | 0.14% |
|2864C-L3FL | 0.07% | 0.16% | 4.15% | 0.12% |
|2867LPS-L1ML | 0.08% | 0.10% | 4.73% | 0.12% |
|2867LPS-L2ML | 0.08% | 0.19% | 4.58% | 0.16% |
|2868LPS-L2ML | 0.08% | 0.09% | 4.06% | 0.13% |
|2870LPS-R1ML | 0.06% | 0.17% | 4.60% | 0.09% |
|2867LPS-R1FL | 0.07% | 0.15% | 4.85% | 0.09% |
|2870LPS-L1FL | 0.08% | 0.17% | 4.82% | 0.11% |
|2870LPS-L2FL | 0.09% | 0.17% | 4.20% | 0.14% |
|2868LPS-R1FL | 0.08% | 0.16% | 3.88% | 0.14% |
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
END OF DOCUMENT
zhezhangsh/Rnaseq documentation built on May 4, 2019, 11:20 p.m.
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title: "Summary of STAR alignment" author: "Jim Zhang" date: "2016-03-28" output: html_document: fig_caption: yes toc: yes toc_float: true
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
Introduction
This report is a summary of STAR runs on a RNA-seq data set. It uses information provided by the *_Log.final.out file generated from each STAR run.
- Output directory: /home/zhangz/R/source/Rnaseq/examples/SummarizeStar/output
- STAR program: /mnt/isilon/cbmi/variome/rnaseq_workspace/tools/STAR-2.5.1b/bin/Linux_x86_64_static/STAR
- Samtools program: /mnt/isilon/cbmi/variome/bin/Samtools/samtools-1.2/samtools
- Passes: 2
- qsub: TRUE
STAR Parameters:
- runThreadN = 8
- readFilesCommand = zcat
- genomeDir = /mnt/isilon/cbmi/variome/rnaseq_workspace/refs/mm38/star
- sjdbGTFfile = /mnt/isilon/cbmi/variome/rnaseq_workspace/refs/mm38/GCF_000001635.24_GRCm38.p4_genomic.gff
- outSAMtype = SAM
- chimSegmentMin = 32
- outFilterType = BySJout
- outFilterMultimapNmax = 20
- alignSJoverhangMin = 8
- alignSJDBoverhangMin = 1
- outFilterMismatchNmax = 999
- outFilterMismatchNoverLmax = 0.04
- alignIntronMin = 20
- alignIntronMax = 1000000
- alignMatesGapMax = 1000000
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
Summary statistics
| | Min.| 1st Qu.| Median| Mean| 3rd Qu.| Max.| |:-------------------------------------|-----:|-------:|------:|--------:|-------:|-----:| |Total input, million reads | 51.71| 55.000| 58.16| 60.06000| 62.0200| 80.45| |Alignment rate (%), unique mapping | 68.20| 78.450| 79.18| 79.13000| 80.1000| 82.15| |Alignment rate (%), unique + multiple | 88.22| 93.810| 94.56| 94.47000| 95.4100| 96.13| |Mismatch rate (%) | 0.16| 0.190| 0.23| 0.22850| 0.2300| 0.48| |Deletion rate (%) | 0.01| 0.010| 0.01| 0.01075| 0.0100| 0.02| |Insertion rate (%) | 0.01| 0.010| 0.01| 0.01025| 0.0100| 0.02| |Too many loci (%) | 0.06| 0.080| 0.14| 0.19400| 0.1800| 2.39| |Too many mismatch (%) | 0.07| 0.110| 0.15| 0.20700| 0.1725| 2.36| |Too short (%) | 3.50| 4.215| 4.86| 4.85700| 5.4320| 6.22|
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
Figures
Alignment rate
Total input vs. uniquely aligned, read count
Unique vs. multiple mapping
Unique vs. multiple mapping, percentage
Non-canonical splice sites
Number of non-canonical splice sites identified from each library
Mismatches and INDELs
Percentage of mismatches and INDELs
Outliers
Outlier reads: mapped to too many loci, too many mismatches, too short, and others
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
Tables
Run information
| | Mapping_star | Mapping_end | Speed | Read_length | Number_reads | |:------------|:---------------:|:---------------:|:-----:|:-----------:|:------------:| |C2863 | Mar 02 22:41:56 | Mar 02 23:37:16 | 61.96 | 200 | 57,140,539 | |C2864 | Mar 02 22:37:35 | Mar 02 23:18:57 | 83.66 | 200 | 57,678,077 | |C2865 | Mar 02 22:39:31 | Mar 02 23:30:15 | 69.19 | 200 | 58,503,755 | |C2866 | Mar 02 22:39:37 | Mar 02 23:25:53 | 75.39 | 200 | 58,135,820 | |LPS2867 | Mar 02 22:35:07 | Mar 02 23:18:04 | 77.59 | 200 | 55,539,026 | |LPS2868 | Mar 02 22:38:00 | Mar 03 06:48:07 | 7.14 | 200 | 58,289,326 | |LPS2869 | Mar 02 22:38:50 | Mar 02 23:34:38 | 63.05 | 200 | 58,639,284 | |LPS2870 | Mar 02 22:42:57 | Mar 02 23:27:47 | 72.12 | 200 | 53,890,556 | |2864C-L1M | Mar 02 22:34:13 | Mar 02 23:25:08 | 69.16 | 200 | 58,689,360 | |2864C-L2M | Mar 02 22:45:31 | Mar 02 23:48:44 | 76.36 | 200 | 80,451,779 | |2865C-L2M | Mar 02 22:48:57 | Mar 02 23:44:53 | 77.86 | 200 | 72,586,064 | |2866C-L1M | Mar 02 22:41:30 | Mar 02 23:21:04 | 83.11 | 200 | 54,809,117 | |2863C-L1F | Mar 02 22:37:58 | Mar 02 23:29:08 | 84.47 | 200 | 72,036,332 | |2863C-L2F | Mar 02 22:42:07 | Mar 02 23:38:33 | 68.68 | 200 | 64,598,433 | |2865C-L1F | Mar 02 22:39:54 | Mar 02 23:31:42 | 70.71 | 200 | 61,046,927 | |2864C-L3F | Mar 02 22:39:11 | Mar 02 23:30:08 | 61.86 | 200 | 52,533,673 | |2867LPS-L1M | Mar 02 22:35:00 | Mar 02 23:23:09 | 79.26 | 200 | 63,604,176 | |2867LPS-L2M | Mar 02 22:38:07 | Mar 02 23:48:53 | 62.72 | 200 | 73,973,748 | |2868LPS-L2M | Mar 02 22:37:08 | Mar 02 23:32:21 | 66.83 | 200 | 61,501,992 | |2870LPS-R1M | Mar 02 22:37:12 | Mar 02 23:29:01 | 82.70 | 200 | 71,419,664 | |2867LPS-R1F | Mar 02 22:38:05 | Mar 02 23:27:38 | 77.52 | 200 | 64,021,829 | |2870LPS-L1F | Mar 02 22:44:27 | Mar 02 23:46:53 | 69.58 | 200 | 72,399,179 | |2870LPS-L2F | Mar 02 22:42:38 | Mar 02 23:28:44 | 71.48 | 200 | 54,921,042 | |2868LPS-R1F | Mar 02 22:37:28 | Mar 02 23:22:14 | 91.67 | 200 | 68,396,671 | |2864C-L1ML | Mar 02 22:50:13 | Mar 02 23:33:09 | 77.39 | 200 | 55,378,147 | |2864C-L2ML | Mar 02 22:35:15 | Mar 02 23:22:40 | 74.22 | 200 | 58,653,865 | |2865C-L2ML | Mar 02 22:43:08 | Mar 02 23:21:02 | 86.34 | 200 | 54,537,485 | |2866C-L1ML | Mar 02 22:39:19 | Mar 02 23:19:38 | 78.92 | 200 | 53,027,128 | |2863C-L1FL | Mar 02 22:41:36 | Mar 02 23:26:29 | 77.56 | 200 | 58,022,655 | |2863C-L2FL | Mar 02 22:39:06 | Mar 02 23:19:47 | 85.57 | 200 | 58,024,246 | |2865C-L1FL | Mar 02 22:38:24 | Mar 02 23:17:47 | 88.65 | 200 | 58,187,304 | |2864C-L3FL | Mar 02 22:37:42 | Mar 02 23:14:32 | 84.23 | 200 | 51,709,700 | |2867LPS-L1ML | Mar 02 23:00:57 | Mar 02 23:43:49 | 80.97 | 200 | 57,847,860 | |2867LPS-L2ML | Mar 02 22:42:27 | Mar 02 23:22:01 | 85.28 | 200 | 56,239,877 | |2868LPS-L2ML | Mar 02 22:46:53 | Mar 02 23:33:36 | 74.99 | 200 | 58,388,067 | |2870LPS-R1ML | Mar 02 22:45:28 | Mar 02 23:29:30 | 74.43 | 200 | 54,620,369 | |2867LPS-R1FL | Mar 02 22:38:29 | Mar 02 23:22:19 | 75.31 | 200 | 55,019,421 | |2870LPS-L1FL | Mar 02 22:40:10 | Mar 02 23:19:37 | 83.02 | 200 | 54,587,346 | |2870LPS-L2FL | Mar 02 22:40:11 | Mar 02 23:16:30 | 90.74 | 200 | 54,919,965 | |2868LPS-R1FL | Mar 02 22:48:19 | Mar 02 23:31:39 | 80.72 | 200 | 58,294,557 |
- Speed: mapping speed, million of reads per hour
Mapping results
Mapped reads, count
| | Input | Unique | Splice | Multiple | Chimeric | |:------------|:----------:|:----------:|:----------:|:----------:|:---------:| |C2863 | 57,140,539 | 45,224,859 | 26,333,237 | 8,024,212 | 1,475,089 | |C2864 | 57,678,077 | 47,383,434 | 25,898,212 | 7,206,858 | 1,256,945 | |C2865 | 58,503,755 | 47,651,274 | 27,994,992 | 7,820,951 | 1,242,161 | |C2866 | 58,135,820 | 47,541,874 | 28,218,827 | 7,804,069 | 1,230,573 | |LPS2867 | 55,539,026 | 43,613,088 | 24,174,654 | 8,430,152 | 1,167,810 | |LPS2868 | 58,289,326 | 39,750,752 | 20,454,935 | 11,667,973 | 1,088,004 | |LPS2869 | 58,639,284 | 45,995,298 | 26,013,427 | 9,211,372 | 1,252,805 | |LPS2870 | 53,890,556 | 42,915,321 | 24,929,460 | 7,858,178 | 1,337,109 | |2864C-L1M | 58,689,360 | 47,001,317 | 26,624,387 | 7,846,028 | 1,272,954 | |2864C-L2M | 80,451,779 | 63,405,469 | 42,143,077 | 11,812,014 | 1,667,531 | |2865C-L2M | 72,586,064 | 57,553,609 | 34,476,997 | 10,537,528 | 1,435,442 | |2866C-L1M | 54,809,117 | 42,934,584 | 24,748,780 | 8,284,712 | 1,332,597 | |2863C-L1F | 72,036,332 | 58,001,207 | 33,989,766 | 10,017,133 | 1,196,370 | |2863C-L2F | 64,598,433 | 51,268,448 | 30,829,437 | 9,443,038 | 1,296,505 | |2865C-L1F | 61,046,927 | 47,967,935 | 29,086,955 | 9,163,766 | 1,220,950 | |2864C-L3F | 52,533,673 | 41,102,200 | 25,438,748 | 7,940,453 | 984,329 | |2867LPS-L1M | 63,604,176 | 49,899,708 | 30,505,878 | 9,933,706 | 1,172,921 | |2867LPS-L2M | 73,973,748 | 58,458,707 | 33,813,429 | 10,802,547 | 1,201,700 | |2868LPS-L2M | 61,501,992 | 48,488,801 | 30,440,441 | 9,205,426 | 1,120,997 | |2870LPS-R1M | 71,419,664 | 56,415,555 | 34,407,365 | 10,795,087 | 1,217,153 | |2867LPS-R1F | 64,021,829 | 50,953,706 | 31,429,140 | 9,503,196 | 1,145,599 | |2870LPS-L1F | 72,399,179 | 57,362,319 | 33,803,580 | 11,048,257 | 1,406,930 | |2870LPS-L2F | 54,921,042 | 43,207,998 | 25,008,930 | 8,579,499 | 1,078,581 | |2868LPS-R1F | 68,396,671 | 55,481,671 | 32,971,296 | 9,589,405 | 1,117,870 | |2864C-L1ML | 55,378,147 | 44,377,346 | 27,240,083 | 8,670,199 | 618,787 | |2864C-L2ML | 58,653,865 | 47,972,002 | 26,608,206 | 8,293,513 | 722,236 | |2865C-L2ML | 54,537,485 | 43,733,356 | 26,619,177 | 8,480,904 | 727,812 | |2866C-L1ML | 53,027,128 | 42,320,800 | 25,685,569 | 8,412,377 | 685,823 | |2863C-L1FL | 58,022,655 | 45,357,738 | 27,277,980 | 10,040,391 | 718,124 | |2863C-L2FL | 58,024,246 | 45,510,473 | 26,615,352 | 9,898,771 | 902,847 | |2865C-L1FL | 58,187,304 | 47,532,703 | 27,206,258 | 8,402,650 | 736,612 | |2864C-L3FL | 51,709,700 | 41,603,095 | 26,594,377 | 7,782,242 | 637,614 | |2867LPS-L1ML | 57,847,860 | 45,148,732 | 26,624,813 | 9,790,283 | 875,730 | |2867LPS-L2ML | 56,239,877 | 44,303,899 | 22,323,854 | 9,119,871 | 748,474 | |2868LPS-L2ML | 58,388,067 | 45,258,906 | 26,402,812 | 10,581,691 | 766,297 | |2870LPS-R1ML | 54,620,369 | 42,614,662 | 27,083,959 | 9,320,797 | 719,779 | |2867LPS-R1FL | 55,019,421 | 42,322,141 | 25,179,090 | 9,858,585 | 830,127 | |2870LPS-L1FL | 54,587,346 | 43,244,708 | 25,303,265 | 8,514,727 | 955,917 | |2870LPS-L2FL | 54,919,965 | 43,882,184 | 25,016,165 | 8,508,797 | 912,717 | |2868LPS-R1FL | 58,294,557 | 46,395,146 | 27,426,807 | 9,418,469 | 679,156 |
- Unique: reads mapped to one and only one genomic loci
- Splice: reads mapped to splice junctions
- Multiple: reads mapped to multiple genomic loci
Mapped reads, percentage
| | Input | Unique | Splice | Multiple | Chimeric | |:------------|:-----:|:------:|:------:|:--------:|:--------:| |C2863 | 100 | 79.15 | 46.09 | 14.04 | 2.58 | |C2864 | 100 | 82.15 | 44.90 | 12.49 | 2.18 | |C2865 | 100 | 81.45 | 47.85 | 13.37 | 2.12 | |C2866 | 100 | 81.78 | 48.54 | 13.42 | 2.12 | |LPS2867 | 100 | 78.53 | 43.53 | 15.18 | 2.10 | |LPS2868 | 100 | 68.20 | 35.09 | 20.02 | 1.87 | |LPS2869 | 100 | 78.44 | 44.36 | 15.71 | 2.14 | |LPS2870 | 100 | 79.63 | 46.26 | 14.58 | 2.48 | |2864C-L1M | 100 | 80.08 | 45.36 | 13.37 | 2.17 | |2864C-L2M | 100 | 78.81 | 52.38 | 14.68 | 2.07 | |2865C-L2M | 100 | 79.29 | 47.50 | 14.52 | 1.98 | |2866C-L1M | 100 | 78.33 | 45.15 | 15.12 | 2.43 | |2863C-L1F | 100 | 80.52 | 47.18 | 13.91 | 1.66 | |2863C-L2F | 100 | 79.36 | 47.72 | 14.62 | 2.01 | |2865C-L1F | 100 | 78.58 | 47.65 | 15.01 | 2.00 | |2864C-L3F | 100 | 78.24 | 48.42 | 15.11 | 1.87 | |2867LPS-L1M | 100 | 78.45 | 47.96 | 15.62 | 1.84 | |2867LPS-L2M | 100 | 79.03 | 45.71 | 14.60 | 1.62 | |2868LPS-L2M | 100 | 78.84 | 49.50 | 14.97 | 1.82 | |2870LPS-R1M | 100 | 78.99 | 48.18 | 15.12 | 1.70 | |2867LPS-R1F | 100 | 79.59 | 49.09 | 14.84 | 1.79 | |2870LPS-L1F | 100 | 79.23 | 46.69 | 15.26 | 1.94 | |2870LPS-L2F | 100 | 78.67 | 45.54 | 15.62 | 1.96 | |2868LPS-R1F | 100 | 81.12 | 48.21 | 14.02 | 1.63 | |2864C-L1ML | 100 | 80.14 | 49.19 | 15.66 | 1.12 | |2864C-L2ML | 100 | 81.79 | 45.36 | 14.14 | 1.23 | |2865C-L2ML | 100 | 80.19 | 48.81 | 15.55 | 1.33 | |2866C-L1ML | 100 | 79.81 | 48.44 | 15.86 | 1.29 | |2863C-L1FL | 100 | 78.17 | 47.01 | 17.30 | 1.24 | |2863C-L2FL | 100 | 78.43 | 45.87 | 17.06 | 1.56 | |2865C-L1FL | 100 | 81.69 | 46.76 | 14.44 | 1.27 | |2864C-L3FL | 100 | 80.46 | 51.43 | 15.05 | 1.23 | |2867LPS-L1ML | 100 | 78.05 | 46.03 | 16.92 | 1.51 | |2867LPS-L2ML | 100 | 78.78 | 39.69 | 16.22 | 1.33 | |2868LPS-L2ML | 100 | 77.51 | 45.22 | 18.12 | 1.31 | |2870LPS-R1ML | 100 | 78.02 | 49.59 | 17.06 | 1.32 | |2867LPS-R1FL | 100 | 76.92 | 45.76 | 17.92 | 1.51 | |2870LPS-L1FL | 100 | 79.22 | 46.35 | 15.60 | 1.75 | |2870LPS-L2FL | 100 | 79.90 | 45.55 | 15.49 | 1.66 | |2868LPS-R1FL | 100 | 79.59 | 47.05 | 16.16 | 1.17 |
Splice sites, count
| | Total | Annotated | GT/AG | GC/AG | AT/AC | Non-canonical | |:------------|:----------:|:----------:|:----------:|:-------:|:------:|:-------------:| |C2863 | 26,333,237 | 26,284,251 | 25,963,802 | 314,477 | 18,300 | 36,658 | |C2864 | 25,898,212 | 25,843,982 | 25,560,618 | 256,138 | 19,278 | 62,178 | |C2865 | 27,994,992 | 27,942,859 | 27,621,298 | 327,762 | 18,908 | 27,024 | |C2866 | 28,218,827 | 28,166,516 | 27,833,989 | 337,013 | 19,509 | 28,316 | |LPS2867 | 24,174,654 | 24,118,600 | 23,813,489 | 290,766 | 16,138 | 54,261 | |LPS2868 | 20,454,935 | 20,380,706 | 20,126,751 | 209,396 | 12,409 | 106,379 | |LPS2869 | 26,013,427 | 25,952,955 | 25,621,642 | 321,513 | 16,618 | 53,654 | |LPS2870 | 24,929,460 | 24,882,986 | 24,593,425 | 271,929 | 17,634 | 46,472 | |2864C-L1M | 26,624,387 | 26,554,452 | 26,355,231 | 193,107 | 20,454 | 55,595 | |2864C-L2M | 42,143,077 | 42,056,254 | 41,746,958 | 298,516 | 27,182 | 70,421 | |2865C-L2M | 34,476,997 | 34,385,277 | 34,121,961 | 258,877 | 26,654 | 69,505 | |2866C-L1M | 24,748,780 | 24,678,243 | 24,488,648 | 194,770 | 19,920 | 45,442 | |2863C-L1F | 33,989,766 | 33,902,132 | 33,634,335 | 254,083 | 25,939 | 75,409 | |2863C-L2F | 30,829,437 | 30,750,920 | 30,506,117 | 226,853 | 22,905 | 73,562 | |2865C-L1F | 29,086,955 | 29,011,712 | 28,791,467 | 219,071 | 21,595 | 54,822 | |2864C-L3F | 25,438,748 | 25,374,273 | 25,178,118 | 184,901 | 18,981 | 56,748 | |2867LPS-L1M | 30,505,878 | 30,417,290 | 30,194,988 | 229,892 | 23,256 | 57,742 | |2867LPS-L2M | 33,813,429 | 33,718,608 | 33,462,679 | 253,626 | 25,054 | 72,070 | |2868LPS-L2M | 30,440,441 | 30,365,104 | 30,121,927 | 241,602 | 22,982 | 53,930 | |2870LPS-R1M | 34,407,365 | 34,312,071 | 34,029,626 | 291,474 | 28,419 | 57,846 | |2867LPS-R1F | 31,429,140 | 31,345,312 | 31,102,441 | 228,886 | 22,915 | 74,898 | |2870LPS-L1F | 33,803,580 | 33,713,782 | 33,446,532 | 276,295 | 25,749 | 55,004 | |2870LPS-L2F | 25,008,930 | 24,939,563 | 24,746,689 | 196,187 | 19,618 | 46,436 | |2868LPS-R1F | 32,971,296 | 32,889,105 | 32,632,029 | 244,181 | 25,010 | 70,076 | |2864C-L1ML | 27,240,083 | 27,200,308 | 26,922,227 | 278,731 | 14,352 | 24,773 | |2864C-L2ML | 26,608,206 | 26,559,204 | 26,285,777 | 278,187 | 15,512 | 28,730 | |2865C-L2ML | 26,619,177 | 26,576,905 | 26,294,250 | 284,647 | 15,800 | 24,480 | |2866C-L1ML | 25,685,569 | 25,641,297 | 25,367,178 | 280,744 | 15,891 | 21,756 | |2863C-L1FL | 27,277,980 | 27,229,163 | 26,934,955 | 301,570 | 17,447 | 24,008 | |2863C-L2FL | 26,615,352 | 26,570,659 | 26,280,666 | 293,676 | 15,383 | 25,627 | |2865C-L1FL | 27,206,258 | 27,159,692 | 26,851,620 | 309,506 | 17,758 | 27,374 | |2864C-L3FL | 26,594,377 | 26,555,264 | 26,295,675 | 261,508 | 14,443 | 22,751 | |2867LPS-L1ML | 26,624,813 | 26,574,570 | 26,258,828 | 317,746 | 16,665 | 31,574 | |2867LPS-L2ML | 22,323,854 | 22,273,295 | 22,004,252 | 274,779 | 14,128 | 30,695 | |2868LPS-L2ML | 26,402,812 | 26,350,260 | 25,993,736 | 363,729 | 18,936 | 26,411 | |2870LPS-R1ML | 27,083,959 | 27,042,790 | 26,730,101 | 313,681 | 16,707 | 23,470 | |2867LPS-R1FL | 25,179,090 | 25,130,573 | 24,830,003 | 307,120 | 16,429 | 25,538 | |2870LPS-L1FL | 25,303,265 | 25,262,204 | 24,994,694 | 264,074 | 15,844 | 28,653 | |2870LPS-L2FL | 25,016,165 | 24,973,046 | 24,698,575 | 272,901 | 16,536 | 28,153 | |2868LPS-R1FL | 27,426,807 | 27,378,227 | 27,062,350 | 319,158 | 18,795 | 26,504 |
Mismatches and INDELs
| | Mismatch_rate | Deletion_rate | Insertion_rate | Avg_deletion_length | Avg_insertion_length | |:------------|:-------------:|:-------------:|:--------------:|:-------------------:|:--------------------:| |C2863 | 0.20% | 0.01% | 0.01% | 2.06 | 1.97 | |C2864 | 0.29% | 0.01% | 0.01% | 2.11 | 1.84 | |C2865 | 0.29% | 0.01% | 0.01% | 2.09 | 1.97 | |C2866 | 0.28% | 0.01% | 0.01% | 2.05 | 1.80 | |LPS2867 | 0.33% | 0.02% | 0.02% | 2.20 | 2.39 | |LPS2868 | 0.48% | 0.02% | 0.01% | 1.92 | 1.94 | |LPS2869 | 0.31% | 0.01% | 0.01% | 2.12 | 2.17 | |LPS2870 | 0.30% | 0.01% | 0.01% | 2.13 | 1.93 | |2864C-L1M | 0.17% | 0.02% | 0.01% | 2.04 | 1.80 | |2864C-L2M | 0.19% | 0.01% | 0.01% | 2.10 | 1.76 | |2865C-L2M | 0.18% | 0.01% | 0.01% | 2.16 | 1.77 | |2866C-L1M | 0.18% | 0.01% | 0.01% | 2.11 | 1.85 | |2863C-L1F | 0.17% | 0.01% | 0.01% | 2.07 | 1.80 | |2863C-L2F | 0.18% | 0.01% | 0.01% | 2.08 | 1.83 | |2865C-L1F | 0.19% | 0.01% | 0.01% | 2.14 | 1.83 | |2864C-L3F | 0.20% | 0.01% | 0.01% | 2.16 | 2.12 | |2867LPS-L1M | 0.23% | 0.01% | 0.01% | 2.17 | 1.83 | |2867LPS-L2M | 0.24% | 0.01% | 0.01% | 2.18 | 2.00 | |2868LPS-L2M | 0.18% | 0.01% | 0.01% | 2.17 | 1.81 | |2870LPS-R1M | 0.23% | 0.01% | 0.01% | 2.23 | 1.89 | |2867LPS-R1F | 0.20% | 0.01% | 0.01% | 2.12 | 1.77 | |2870LPS-L1F | 0.20% | 0.01% | 0.01% | 2.16 | 1.87 | |2870LPS-L2F | 0.20% | 0.01% | 0.01% | 2.17 | 2.08 | |2868LPS-R1F | 0.19% | 0.01% | 0.01% | 2.16 | 1.90 | |2864C-L1ML | 0.23% | 0.01% | 0.01% | 2.14 | 1.65 | |2864C-L2ML | 0.23% | 0.01% | 0.01% | 2.13 | 1.68 | |2865C-L2ML | 0.23% | 0.01% | 0.01% | 2.12 | 1.68 | |2866C-L1ML | 0.22% | 0.01% | 0.01% | 2.09 | 1.67 | |2863C-L1FL | 0.23% | 0.01% | 0.01% | 2.08 | 1.68 | |2863C-L2FL | 0.16% | 0.01% | 0.01% | 2.05 | 1.61 | |2865C-L1FL | 0.23% | 0.01% | 0.01% | 2.14 | 1.66 | |2864C-L3FL | 0.23% | 0.01% | 0.01% | 2.14 | 1.65 | |2867LPS-L1ML | 0.19% | 0.01% | 0.01% | 2.24 | 1.68 | |2867LPS-L2ML | 0.23% | 0.01% | 0.01% | 2.23 | 1.69 | |2868LPS-L2ML | 0.19% | 0.01% | 0.01% | 2.18 | 1.70 | |2870LPS-R1ML | 0.24% | 0.01% | 0.01% | 2.16 | 1.63 | |2867LPS-R1FL | 0.23% | 0.01% | 0.01% | 2.16 | 1.57 | |2870LPS-L1FL | 0.23% | 0.01% | 0.01% | 2.07 | 1.61 | |2870LPS-L2FL | 0.23% | 0.01% | 0.01% | 2.10 | 1.64 | |2868LPS-R1FL | 0.23% | 0.01% | 0.01% | 2.18 | 1.70 |
- Rates are per base
Outliers
| | Too_many_loci | Too_many_mismatch | Too_short | Other | |:------------|:-------------:|:-----------------:|:---------:|:-----:| |C2863 | 0.26% | 0.17% | 6.22% | 0.16% | |C2864 | 0.20% | 0.18% | 4.78% | 0.19% | |C2865 | 0.20% | 0.21% | 4.62% | 0.16% | |C2866 | 0.19% | 0.13% | 4.36% | 0.12% | |LPS2867 | 0.26% | 0.41% | 5.51% | 0.12% | |LPS2868 | 2.39% | 2.36% | 5.22% | 1.83% | |LPS2869 | 0.30% | 0.29% | 5.13% | 0.14% | |LPS2870 | 0.27% | 0.19% | 5.21% | 0.11% | |2864C-L1M | 0.18% | 0.15% | 5.73% | 0.49% | |2864C-L2M | 0.18% | 0.10% | 5.89% | 0.34% | |2865C-L2M | 0.16% | 0.10% | 5.47% | 0.46% | |2866C-L1M | 0.14% | 0.11% | 5.96% | 0.34% | |2863C-L1F | 0.14% | 0.08% | 4.91% | 0.45% | |2863C-L2F | 0.14% | 0.10% | 5.42% | 0.36% | |2865C-L1F | 0.13% | 0.12% | 5.87% | 0.30% | |2864C-L3F | 0.19% | 0.20% | 5.84% | 0.42% | |2867LPS-L1M | 0.16% | 0.11% | 5.31% | 0.35% | |2867LPS-L2M | 0.18% | 0.20% | 5.56% | 0.43% | |2868LPS-L2M | 0.14% | 0.10% | 5.60% | 0.34% | |2870LPS-R1M | 0.12% | 0.12% | 5.42% | 0.24% | |2867LPS-R1F | 0.15% | 0.11% | 4.87% | 0.43% | |2870LPS-L1F | 0.16% | 0.13% | 4.90% | 0.32% | |2870LPS-L2F | 0.15% | 0.18% | 5.04% | 0.34% | |2868LPS-R1F | 0.14% | 0.12% | 4.22% | 0.39% | |2864C-L1ML | 0.07% | 0.15% | 3.85% | 0.14% | |2864C-L2ML | 0.08% | 0.15% | 3.67% | 0.17% | |2865C-L2ML | 0.08% | 0.15% | 3.88% | 0.15% | |2866C-L1ML | 0.07% | 0.14% | 4.02% | 0.10% | |2863C-L1FL | 0.08% | 0.14% | 4.20% | 0.11% | |2863C-L2FL | 0.08% | 0.07% | 4.24% | 0.12% | |2865C-L1FL | 0.08% | 0.15% | 3.50% | 0.14% | |2864C-L3FL | 0.07% | 0.16% | 4.15% | 0.12% | |2867LPS-L1ML | 0.08% | 0.10% | 4.73% | 0.12% | |2867LPS-L2ML | 0.08% | 0.19% | 4.58% | 0.16% | |2868LPS-L2ML | 0.08% | 0.09% | 4.06% | 0.13% | |2870LPS-R1ML | 0.06% | 0.17% | 4.60% | 0.09% | |2867LPS-R1FL | 0.07% | 0.15% | 4.85% | 0.09% | |2870LPS-L1FL | 0.08% | 0.17% | 4.82% | 0.11% | |2870LPS-L2FL | 0.09% | 0.17% | 4.20% | 0.14% | |2868LPS-R1FL | 0.08% | 0.16% | 3.88% | 0.14% |
**_[Go back to project home](http://mybic.chop.edu/labs/Rebecca_Simmons_Lab/Infant_mouse_LPS)_**
END OF DOCUMENT
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