BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716458.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 = 2,621,028 number of mapped reads = 2,350,967 (89.7%) number of supplementary alignments = 8,902 (0.34%) number of secondary alignments = 0 number of mapped bases = 135,722,116 bp number of sequenced bases = 135,680,492 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,488 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0109 >>>>>>> ACTG content number of A's = 33,531,015 bp (24.71%) number of C's = 27,312,475 bp (20.13%) number of T's = 41,674,636 bp (30.72%) number of G's = 33,161,198 bp (24.44%) number of N's = 1,168 bp (0%) GC percentage = 44.57% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 713,475 number of insertions = 10,825 mapped reads with insertion percentage = 0.46% number of deletions = 26,156 mapped reads with deletion percentage = 1.1% homopolymer indels = 39.52% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.3361X There is a 3.76% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10854414 0.04354819240350057 0.4424891192572485 chr2 243199373 11272836 0.04635224121239819 0.5293626071631385 chr3 198022430 9103167 0.045970383254058646 0.24884161734181617 chr4 191154276 8642644 0.04521292529182031 0.2841136240422615 chr5 180915260 8088962 0.04471133059754053 0.2407474275725364 chr6 171115067 7785886 0.04550087924168595 0.2856522538981997 chr7 159138663 7451854 0.04682616945198289 0.4232101263064988 chr8 146364022 6774569 0.046285753202381937 0.3331632307116077 chr9 141213431 5772701 0.04087926310635424 0.2883539533847089 chr10 135534747 6559669 0.048398430256412404 0.4199250951603132 chr11 135006516 6032869 0.044685761685754485 0.3075379721474677 chr12 133851895 6200182 0.04632121196341673 0.2485215701894546 chr13 115169878 4209666 0.03655179698983444 0.21859818488790592 chr14 107349540 4142723 0.038590971139699344 0.23940208878475894 chr15 102531392 3962845 0.03865006533803813 0.22830670327258998 chr16 90354753 4033934 0.04464550968336995 0.26706299697771557 chr17 81195210 3895758 0.04798014562681715 0.2670040855587672 chr18 78077248 3505918 0.04490319638315121 0.45342884323004956 chr19 59128983 2978580 0.05037428091736332 0.4005388691241747 chr20 63025520 2955749 0.046897653521938414 0.2563476008531839 chr21 48129895 1771450 0.036805606993325045 0.2553022468012241 chr22 51304566 1686507 0.0328724542762919 0.21001659364909103 chrMT 16571 50999 3.0776054553134995 2.6273770794325886 chrX 155270560 7557534 0.04867332223185129 0.2758659148346821 chrY 59373566 430700 0.007254069934084808 0.2090319335292779