BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004065.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,168,426 number of mapped reads = 969,356 (82.96%) number of supplementary alignments = 8,344 (0.71%) number of secondary alignments = 0 number of mapped bases = 64,173,310 bp number of sequenced bases = 64,128,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,547 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7725 >>>>>>> ACTG content number of A's = 18,472,278 bp (28.8%) number of C's = 11,339,790 bp (17.68%) number of T's = 20,550,528 bp (32.05%) number of G's = 13,724,161 bp (21.4%) number of N's = 42,239 bp (0.07%) GC percentage = 39.08% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 660,840 number of insertions = 5,318 mapped reads with insertion percentage = 0.54% number of deletions = 26,014 mapped reads with deletion percentage = 2.64% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2237X There is a 1.86% 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 4257009 0.017079231268996516 0.3631410097289089 chr2 243199373 3952293 0.016251246667482157 0.20455282292452517 chr3 198022430 3620198 0.01828175727365834 0.14749750245000495 chr4 191154276 4137803 0.02164640564985321 0.16334131501193455 chr5 180915260 3405609 0.018824332452663198 0.14871638567800233 chr6 171115067 4407742 0.025758935652346732 0.19124427513171566 chr7 159138663 3379394 0.021235530928144092 0.24939579398307796 chr8 146364022 5147554 0.035169530938416 0.3958477814971681 chr9 141213431 1877286 0.013293962101947655 0.18487295520049535 chr10 135534747 3502412 0.02584143238191163 0.25633944440394196 chr11 135006516 2403636 0.017803851778531932 0.1747067805329117 chr12 133851895 3895707 0.02910460849284203 0.18491141887720186 chr13 115169878 1985751 0.017241930220678013 0.1405621229456184 chr14 107349540 1546745 0.014408492109048628 0.1374386396956042 chr15 102531392 2551281 0.024882925611699486 0.17235796602339284 chr16 90354753 1195551 0.013231744432968567 0.15135174228680578 chr17 81195210 1494555 0.018406935581544773 0.15347532156357618 chr18 78077248 1830273 0.023441822642109516 0.36299848936610646 chr19 59128983 928225 0.015698308222213124 0.2467491999140161 chr20 63025520 1615826 0.025637646464479785 0.178740526838191 chr21 48129895 691619 0.014369842277860777 0.13601373457557037 chr22 51304566 535172 0.010431274284631899 0.109148777715706 chrMT 16571 25881 1.5618248747812444 1.6575710050210006 chrX 155270560 5569449 0.035869317403118786 0.2201066223057203 chrY 59373566 216339 0.0036436922114464203 0.091239839159494