BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524637.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 = 870,362 number of mapped reads = 797,255 (91.6%) number of supplementary alignments = 3,435 (0.39%) number of secondary alignments = 0 number of mapped bases = 46,559,967 bp number of sequenced bases = 46,544,432 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,835 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8664 >>>>>>> ACTG content number of A's = 11,844,330 bp (25.45%) number of C's = 8,391,469 bp (18.03%) number of T's = 14,562,198 bp (31.29%) number of G's = 11,746,006 bp (25.24%) number of N's = 429 bp (0%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 225,526 number of insertions = 3,750 mapped reads with insertion percentage = 0.47% number of deletions = 9,115 mapped reads with deletion percentage = 1.13% homopolymer indels = 40.47% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.1617X There is a 1.39% of reference with a coverageData >= 1X There is a 0.09% 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 4882310 0.0195879552091467 0.2642706441973968 chr2 243199373 3873752 0.01592829764408973 0.1841629437876631 chr3 198022430 2970980 0.01500324988436916 0.13065909860866354 chr4 191154276 2107099 0.011023028331314964 0.12446937704073163 chr5 180915260 2723109 0.015051848030951066 0.12997458721091293 chr6 171115067 2994638 0.017500726572488207 0.1452131054590712 chr7 159138663 2841801 0.017857388936339123 0.19028206642898665 chr8 146364022 4100825 0.028017985184911085 0.21535514253504442 chr9 141213431 1782215 0.012620718775680764 0.1357316522619208 chr10 135534747 2106251 0.015540302738750823 0.17702745946399506 chr11 135006516 2450667 0.018152212742087205 0.1547903385032268 chr12 133851895 1423160 0.010632348537164901 0.11131922872972835 chr13 115169878 1118463 0.009711419508493357 0.10424454638529132 chr14 107349540 841554 0.007839381519473675 0.09870656509047455 chr15 102531392 1149873 0.011214838476005476 0.11335269499507819 chr16 90354753 1470318 0.016272724468628673 0.13933342343895475 chr17 81195210 1101542 0.013566588472398803 0.12634337707108273 chr18 78077248 1132050 0.014499102222455382 0.19767605970823002 chr19 59128983 1045222 0.017676982538326426 0.2055087267320672 chr20 63025520 905056 0.014360151253016238 0.12953291498942318 chr21 48129895 383432 0.007966607863989731 0.10793712275590707 chr22 51304566 1027547 0.02002837330307014 0.15109481453290632 chrMT 16571 7876 0.4752881540039829 0.77131883413659 chrX 155270560 1993704 0.012840193272955285 0.1269142079641629 chrY 59373566 126523 0.00213096515038359 0.08435683282816865