BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081928.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,840,838 number of mapped reads = 2,591,417 (91.22%) number of supplementary alignments = 13,779 (0.49%) number of secondary alignments = 0 number of mapped bases = 177,395,033 bp number of sequenced bases = 177,324,370 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,148 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5289 >>>>>>> ACTG content number of A's = 50,417,838 bp (28.43%) number of C's = 32,918,001 bp (18.56%) number of T's = 55,726,041 bp (31.43%) number of G's = 38,239,575 bp (21.56%) number of N's = 22,915 bp (0.01%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,406,038 number of insertions = 13,169 mapped reads with insertion percentage = 0.5% number of deletions = 40,062 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.0573X std coverageData = 0.5826X There is a 4.9% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% 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 16282477 0.06532572289960313 1.1610436419754506 chr2 243199373 15844646 0.065150850532826 0.7243627179059421 chr3 198022430 11014469 0.05562233025824398 0.26886171228670863 chr4 191154276 9123685 0.04772943190661348 0.2846684048740608 chr5 180915260 9099308 0.05029596729430121 0.25681061871218935 chr6 171115067 15453801 0.09031233351298047 0.4919311482148257 chr7 159138663 11827370 0.07432115978000896 0.8534117748896889 chr8 146364022 10082503 0.06888648495871479 0.6933362349510742 chr9 141213431 8526878 0.06038291074451693 0.6100257415578202 chr10 135534747 7248697 0.05348220408748762 0.5872919182578853 chr11 135006516 8077571 0.0598309714177055 0.39783403155865255 chr12 133851895 7271169 0.05432249577041849 0.2757275591028489 chr13 115169878 4769084 0.04140912609111212 0.22761300714666938 chr14 107349540 4509374 0.04200645852790799 0.28982945460416076 chr15 102531392 4134246 0.04032175823771124 0.22911733270443616 chr16 90354753 3925474 0.04344513010842938 0.31243055824776306 chr17 81195210 4687823 0.057735216153760795 0.306284788297018 chr18 78077248 4530528 0.05802622551450584 1.0110274966276331 chr19 59128983 3855474 0.06520447003121972 0.8132924406852065 chr20 63025520 4545929 0.07212838545401926 0.31707418180673247 chr21 48129895 1901370 0.039504968793304035 0.27267809830931755 chr22 51304566 1392118 0.027134387999695777 0.18022167545195092 chrMT 16571 19476 1.1753062579204634 1.3256516731530177 chrX 155270560 8847384 0.05698043466836212 0.3272688227142872 chrY 59373566 424179 0.007144239913095333 0.19242801505145438