BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717092.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 = 695,844 number of mapped reads = 584,191 (83.95%) number of supplementary alignments = 2,506 (0.36%) number of secondary alignments = 0 number of mapped bases = 32,778,216 bp number of sequenced bases = 32,768,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,883 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5377 >>>>>>> ACTG content number of A's = 7,959,744 bp (24.29%) number of C's = 6,317,503 bp (19.28%) number of T's = 10,323,095 bp (31.5%) number of G's = 8,167,804 bp (24.93%) number of N's = 501 bp (0%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 172,795 number of insertions = 1,906 mapped reads with insertion percentage = 0.32% number of deletions = 6,040 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.02% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 0.1264X There is a 1% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2393782 0.009603915891547568 0.13920687222739148 chr2 243199373 3232302 0.013290749725740453 0.16584609349097487 chr3 198022430 2332696 0.011779958462281267 0.11543911289423152 chr4 191154276 2044423 0.010695146573650281 0.10960318375384132 chr5 180915260 1712062 0.009463336591949182 0.10090819465658807 chr6 171115067 1815182 0.010607961249841313 0.11143857694596947 chr7 159138663 1649423 0.010364690571768849 0.20247255578678697 chr8 146364022 2609148 0.01782643004986567 0.14750105417933804 chr9 141213431 1377756 0.009756550706568414 0.10937777388818887 chr10 135534747 1584366 0.011689740343854407 0.1463773594591582 chr11 135006516 1119454 0.008291851631813089 0.1040212953559625 chr12 133851895 1557135 0.011633268247715134 0.11444399183028127 chr13 115169878 861563 0.007480801533887185 0.08952178569065021 chr14 107349540 995656 0.009274897684703633 0.10096193985087004 chr15 102531392 751458 0.007329052940196111 0.08951436036326495 chr16 90354753 1028875 0.011387060069767443 0.11304285480175437 chr17 81195210 1448118 0.017835017607565767 0.14180642017050724 chr18 78077248 742820 0.00951391114604859 0.12893730336777354 chr19 59128983 736588 0.01245730879558676 0.14519373232223745 chr20 63025520 724912 0.011501880508086247 0.11182066729353847 chr21 48129895 349421 0.007259957662488148 0.08889419633911998 chr22 51304566 478256 0.009321899341278903 0.10069907767619478 chrMT 16571 11199 0.6758192022207471 0.8854662585901706 chrX 155270560 1149901 0.007405788966047395 0.09748749457535806 chrY 59373566 71720 0.0012079449632518282 0.04439009491112557