BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472581.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 10,080,520 number of mapped reads = 9,240,683 (91.67%) number of supplementary alignments = 282,769 (2.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,664,511 number of mapped paired reads (second in pair) = 4,576,172 number of mapped paired reads (both in pair) = 9,016,940 number of mapped paired reads (singletons) = 223,743 number of mapped bases = 751,782,918 bp number of sequenced bases = 751,470,186 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,469,508 duplication rate = 13.42% >>>>>>> Insert size mean insert size = 232,585.4248 std insert size = 4,621,951.0073 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 50.7115 >>>>>>> ACTG content number of A's = 195,572,790 bp (26.03%) number of C's = 147,609,011 bp (19.64%) number of T's = 226,493,201 bp (30.14%) number of G's = 181,285,813 bp (24.12%) number of N's = 509,371 bp (0.07%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 8,996,765 number of insertions = 69,948 mapped reads with insertion percentage = 0.74% number of deletions = 168,490 mapped reads with deletion percentage = 1.79% homopolymer indels = 43.17% >>>>>>> Coverage mean coverageData = 0.2428X std coverageData = 2.3937X There is a 12.89% of reference with a coverageData >= 1X There is a 5.92% of reference with a coverageData >= 2X There is a 2.28% of reference with a coverageData >= 3X There is a 1.13% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 46331903 0.18588480467617371 3.029463008706929 chr2 243199373 74030208 0.3044013111004197 3.8569389281414694 chr3 198022430 41847127 0.21132518674778408 0.7130177508407379 chr4 191154276 41599756 0.21762398869905478 1.2095183008242905 chr5 180915260 35809354 0.19793440310120883 0.7790198687547483 chr6 171115067 51176993 0.2990794083609248 1.5294979994981979 chr7 159138663 58766908 0.3692811469705511 3.839919026885904 chr8 146364022 39296888 0.2684873472525919 2.137663965581895 chr9 141213431 24011985 0.1700403766834332 2.8228432924593334 chr10 135534747 30369602 0.224072443946791 2.100178460843795 chr11 135006516 28487058 0.21100505993355165 1.9686200759880634 chr12 133851895 38870576 0.2903998931057345 0.8791964336242859 chr13 115169878 37723912 0.3275501602945173 0.9504410002959226 chr14 107349540 18245178 0.16996046745985124 4.794568905177785 chr15 102531392 18689434 0.1822801157327504 0.6800943037610961 chr16 90354753 27641727 0.3059244376441381 1.2838472222136172 chr17 81195210 25978269 0.31994829497946986 2.1902610206811297 chr18 78077248 17958558 0.23001013048000873 4.65289873708628 chr19 59128983 14090101 0.23829432344540746 2.1615882479460753 chr20 63025520 24875840 0.3946947204878278 1.3253395266205548 chr21 48129895 11863030 0.24647944899942126 1.0465765545937615 chr22 51304566 7282779 0.14195186837756313 0.6029342971949099 chrMT 16571 190152 11.47498642206264 7.548999834949095 chrX 155270560 35099148 0.2260515322415273 1.1383836595484822 chrY 59373566 1546432 0.026045799573500436 0.9354331486639618