BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961019.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 307,638,920 number of mapped reads = 300,522,777 (97.69%) number of supplementary alignments = 690,991 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 150,433,105 number of mapped paired reads (second in pair) = 150,089,672 number of mapped paired reads (both in pair) = 299,539,418 number of mapped paired reads (singletons) = 983,359 number of mapped bases = 29,522,158,888 bp number of sequenced bases = 29,512,967,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,487,537 duplication rate = 8.4% >>>>>>> Insert size mean insert size = 21,824.3266 std insert size = 1,383,627.9771 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.6615 >>>>>>> ACTG content number of A's = 8,693,007,240 bp (29.45%) number of C's = 6,042,003,144 bp (20.47%) number of T's = 8,671,319,857 bp (29.38%) number of G's = 6,091,693,901 bp (20.64%) number of N's = 14,942,967 bp (0.05%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 141,508,678 number of insertions = 3,054,022 mapped reads with insertion percentage = 0.98% number of deletions = 3,624,218 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.64% >>>>>>> Coverage mean coverageData = 9.5365X std coverageData = 104.6401X There is a 91.44% of reference with a coverageData >= 1X There is a 90.87% of reference with a coverageData >= 2X There is a 89.62% of reference with a coverageData >= 3X There is a 87.34% of reference with a coverageData >= 4X There is a 83.64% of reference with a coverageData >= 5X There is a 78.38% of reference with a coverageData >= 6X There is a 71.6% of reference with a coverageData >= 7X There is a 63.6% of reference with a coverageData >= 8X There is a 54.87% of reference with a coverageData >= 9X There is a 45.95% of reference with a coverageData >= 10X There is a 37.37% of reference with a coverageData >= 11X There is a 29.53% of reference with a coverageData >= 12X There is a 22.71% of reference with a coverageData >= 13X There is a 17.02% of reference with a coverageData >= 14X There is a 12.47% of reference with a coverageData >= 15X There is a 8.94% of reference with a coverageData >= 16X There is a 6.31% of reference with a coverageData >= 17X There is a 4.4% of reference with a coverageData >= 18X There is a 3.04% of reference with a coverageData >= 19X There is a 2.11% of reference with a coverageData >= 20X There is a 1.47% of reference with a coverageData >= 21X There is a 1.05% of reference with a coverageData >= 22X There is a 0.77% of reference with a coverageData >= 23X There is a 0.59% of reference with a coverageData >= 24X There is a 0.47% of reference with a coverageData >= 25X There is a 0.39% of reference with a coverageData >= 26X There is a 0.33% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2402862638 9.640347648321406 248.8721572785932 chr2 243199373 2527920151 10.394435313778544 65.35292468497329 chr3 198022430 1941252814 9.803196607576222 21.48224691083403 chr4 191154276 1986226641 10.390699504938095 92.06119122636419 chr5 180915260 1770829260 9.788169665731902 10.179878442680067 chr6 171115067 1686899945 9.858278260207209 30.424129461085503 chr7 159138663 1575426478 9.899709148618397 64.42417229905605 chr8 146364022 1481336618 10.120906748517747 101.49369133049072 chr9 141213431 1231834239 8.723208764752696 89.29704832272935 chr10 135534747 1544370392 11.394645477886199 246.56718066836868 chr11 135006516 1329778292 9.849734156535082 41.374505784884626 chr12 133851895 1300886406 9.718849374526972 8.076850900993323 chr13 115169878 936460350 8.131122184569824 5.886329746934484 chr14 107349540 869136138 8.096319164478954 9.368298034750756 chr15 102531392 819269581 7.990426785583873 6.047581941060747 chr16 90354753 948894414 10.501876021950943 101.0074450569209 chr17 81195210 791571276 9.74898982341446 38.78471266467641 chr18 78077248 803095339 10.285907349090992 107.00475988074203 chr19 59128983 577265655 9.762820628929132 120.6172439414144 chr20 63025520 608732760 9.658512297875527 34.40861199960289 chr21 48129895 405438764 8.423844764257225 46.13091039790905 chr22 51304566 347290373 6.769190348476975 8.104345939825508 chrMT 16571 22709803 1370.4545893428278 194.11284527934376 chrX 155270560 1513429651 9.747048320042126 31.472176513568606 chrY 59373566 99240910 1.6714662211799776 98.01570729511353