BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716793.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 = 600,310 number of mapped reads = 516,204 (85.99%) number of supplementary alignments = 534 (0.09%) number of secondary alignments = 0 number of mapped bases = 27,304,689 bp number of sequenced bases = 27,297,231 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,383 duplication rate = 5.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0174 >>>>>>> ACTG content number of A's = 5,645,136 bp (20.68%) number of C's = 4,875,531 bp (17.86%) number of T's = 8,474,765 bp (31.05%) number of G's = 8,301,349 bp (30.41%) number of N's = 450 bp (0%) GC percentage = 48.27% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 168,707 number of insertions = 1,421 mapped reads with insertion percentage = 0.27% number of deletions = 4,241 mapped reads with deletion percentage = 0.81% homopolymer indels = 42.83% >>>>>>> Coverage mean coverageData = 0.0088X std coverageData = 0.1103X There is a 0.79% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 2702679 0.010843218721609524 0.1298159738126041 chr2 243199373 2342047 0.009630152294841649 0.13290381148608757 chr3 198022430 1794365 0.00906142299132477 0.1045761526563029 chr4 191154276 1726466 0.009031793774783255 0.10724500358462252 chr5 180915260 1642161 0.00907696233031973 0.10466402080504812 chr6 171115067 1149124 0.006715504485645323 0.0936951999556417 chr7 159138663 1571001 0.009871900205671578 0.11671746575880126 chr8 146364022 1680966 0.011484830609533264 0.12006803570003095 chr9 141213431 1192424 0.008444125969859056 0.10565289253898748 chr10 135534747 1419911 0.010476361460282949 0.12347239529082567 chr11 135006516 1184846 0.008776213438468407 0.10924008626075189 chr12 133851895 1308617 0.009776604208703956 0.10947142538834918 chr13 115169878 464224 0.004030776172221004 0.07089540814159243 chr14 107349540 871456 0.008117929522567121 0.09903645204788322 chr15 102531392 535162 0.005219494142827984 0.07974266061818248 chr16 90354753 752978 0.008333573774475373 0.10616379307209933 chr17 81195210 1115706 0.013741032260400583 0.13471226079005177 chr18 78077248 713647 0.00914026836601618 0.11398438846261956 chr19 59128983 767909 0.012987015183399992 0.14631706444006265 chr20 63025520 770466 0.012224667087237044 0.12836309720233202 chr21 48129895 381172 0.007919651601151425 0.10205147811094488 chr22 51304566 330259 0.006437224320346068 0.09339800051759697 chrMT 16571 502 0.030293886910868383 0.17139477041817788 chrX 155270560 809463 0.0052132419693726876 0.07980125645165431 chrY 59373566 77138 0.0012991976934651356 0.04981133734073936