BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716811.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 = 1,454,739 number of mapped reads = 1,306,634 (89.82%) number of supplementary alignments = 5,930 (0.41%) number of secondary alignments = 0 number of mapped bases = 75,855,807 bp number of sequenced bases = 75,833,954 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,079 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9669 >>>>>>> ACTG content number of A's = 18,217,552 bp (24.02%) number of C's = 14,123,556 bp (18.62%) number of T's = 24,415,938 bp (32.2%) number of G's = 19,074,801 bp (25.15%) number of N's = 2,107 bp (0%) GC percentage = 43.78% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 374,046 number of insertions = 4,926 mapped reads with insertion percentage = 0.38% number of deletions = 13,878 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.96% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.2352X There is a 2.23% of reference with a coverageData >= 1X There is a 0.17% 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 8523839 0.034197864646443546 0.42368192222818757 chr2 243199373 6904140 0.02838880674252396 0.29846981159299085 chr3 198022430 6813283 0.03440662252250919 0.2013769480188843 chr4 191154276 3536940 0.018503065032141892 0.15447737554594176 chr5 180915260 3307711 0.01828320618172287 0.1472849143286858 chr6 171115067 5370457 0.0313850620763863 0.24795316491423627 chr7 159138663 4319098 0.02714046931511546 0.2812969295792038 chr8 146364022 5022069 0.034312182265666354 0.2230217110513169 chr9 141213431 2864386 0.020284090399304865 0.1937719255986706 chr10 135534747 3933502 0.02902209276267731 0.24438502350895625 chr11 135006516 2566980 0.01901374893638467 0.18129269145109708 chr12 133851895 3376998 0.025229362647424602 0.17484164396442342 chr13 115169878 1748110 0.015178534790147125 0.13621492662114681 chr14 107349540 1663617 0.01549719728654636 0.14278455610981103 chr15 102531392 2255043 0.021993683651539617 0.16214143691595298 chr16 90354753 1573490 0.01741457917548621 0.16053353382088148 chr17 81195210 1660965 0.020456440718608894 0.15891506497560953 chr18 78077248 1478849 0.018940844328939464 0.3475855231141326 chr19 59128983 1580604 0.026731459257467696 0.29058016428825884 chr20 63025520 1167975 0.01853177887306602 0.14828954574096712 chr21 48129895 700687 0.01455824908822261 0.13871999223712975 chr22 51304566 1218232 0.023745099022960257 0.1663550957137246 chrMT 16571 31516 1.9018767726751553 1.7376695463360181 chrX 155270560 4055212 0.026117069456051425 0.19420109416003808 chrY 59373566 182104 0.003067088811879684 0.07760778336951955