BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716871.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,443,683 number of mapped reads = 1,303,411 (90.28%) number of supplementary alignments = 7,095 (0.49%) number of secondary alignments = 0 number of mapped bases = 75,528,254 bp number of sequenced bases = 75,506,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,438 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.501 >>>>>>> ACTG content number of A's = 18,215,168 bp (24.12%) number of C's = 14,160,317 bp (18.75%) number of T's = 24,191,249 bp (32.04%) number of G's = 18,937,660 bp (25.08%) number of N's = 1,938 bp (0%) GC percentage = 43.83% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 379,387 number of insertions = 4,874 mapped reads with insertion percentage = 0.37% number of deletions = 13,924 mapped reads with deletion percentage = 1.06% homopolymer indels = 44.21% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2311X There is a 2.23% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 8569111 0.03437949709260704 0.39436763969034117 chr2 243199373 6421862 0.02640575064311535 0.29975236603983646 chr3 198022430 6888331 0.034785609892778305 0.2023659678556362 chr4 191154276 3592921 0.018795922723695704 0.1533415090679519 chr5 180915260 3351478 0.01852512607283653 0.1471848739097459 chr6 171115067 5423554 0.03169536204547084 0.24996754205782068 chr7 159138663 4357571 0.02738222703303722 0.2806523094624334 chr8 146364022 5020880 0.034304058684585755 0.2190845022510128 chr9 141213431 2860873 0.02025921316223809 0.19860534683291503 chr10 135534747 3926283 0.02896882966845395 0.2589911667565686 chr11 135006516 2550858 0.01889433247799684 0.18749298817648744 chr12 133851895 3375549 0.025218537249696762 0.17263042165811174 chr13 115169878 1703223 0.014788788783817241 0.13079563268312316 chr14 107349540 1681146 0.015660486295516498 0.14460945898575353 chr15 102531392 2250230 0.021946741930510414 0.16174328944690247 chr16 90354753 1588658 0.017582450809200928 0.1639634184340164 chr17 81195210 1665939 0.020517700489967327 0.1594088610379941 chr18 78077248 1499698 0.019207874744765593 0.3315434026778805 chr19 59128983 1579135 0.02670661526513994 0.2812750521211823 chr20 63025520 1151439 0.018269408963226326 0.1451614443803314 chr21 48129895 664061 0.01379726675073777 0.14057691633095454 chr22 51304566 1217066 0.023722372000963814 0.1655242323279825 chrMT 16571 10890 0.6571721682457305 0.841407328496178 chrX 155270560 3993553 0.025719962625239453 0.1923918565287933 chrY 59373566 183945 0.003098095876538728 0.07604308770672122