BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716931.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 = 1,112,521 number of mapped reads = 898,413 (80.75%) number of supplementary alignments = 3,123 (0.28%) number of secondary alignments = 0 number of mapped bases = 50,807,755 bp number of sequenced bases = 50,792,175 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,813 duplication rate = 1.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9523 >>>>>>> ACTG content number of A's = 13,156,297 bp (25.9%) number of C's = 9,296,779 bp (18.3%) number of T's = 15,816,067 bp (31.14%) number of G's = 12,522,305 bp (24.65%) number of N's = 727 bp (0%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 256,383 number of insertions = 4,463 mapped reads with insertion percentage = 0.49% number of deletions = 10,025 mapped reads with deletion percentage = 1.11% homopolymer indels = 37.15% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 0.1809X There is a 1.53% of reference with a coverageData >= 1X There is a 0.08% 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 3925200 0.015748004896645774 0.20095520192334934 chr2 243199373 4677110 0.019231587410383662 0.2072395743869436 chr3 198022430 3687947 0.018623885183107793 0.1501695741428065 chr4 191154276 2734363 0.014304482521751174 0.12840619462258243 chr5 180915260 3675793 0.020317760922986816 0.149311759535632 chr6 171115067 2719129 0.015890646263195515 0.14080163964782516 chr7 159138663 3455229 0.02171206503098496 0.41290693343707485 chr8 146364022 3779511 0.02582267792559021 0.19182889621178448 chr9 141213431 1898793 0.01344626347900293 0.13760304676808138 chr10 135534747 2373586 0.01751274896318654 0.2130929379655439 chr11 135006516 1812189 0.013422974339994079 0.14261521093514487 chr12 133851895 2175729 0.016254749325737974 0.13825928054248754 chr13 115169878 1295078 0.011244936805437963 0.11175151419073155 chr14 107349540 1216251 0.011329820323403341 0.11411392773904282 chr15 102531392 1373297 0.013393917445302996 0.1242267592903424 chr16 90354753 1618109 0.017908399351166397 0.14469237329242363 chr17 81195210 1936975 0.02385577917712141 0.16784598897719888 chr18 78077248 1093617 0.014006858950766298 0.17646559199830483 chr19 59128983 952513 0.016109071248527985 0.21210926295813576 chr20 63025520 1036719 0.01644919391383046 0.1359860884982597 chr21 48129895 569043 0.01182306755499882 0.11613247473951303 chr22 51304566 706379 0.013768345686814698 0.12335297842985744 chrMT 16571 8224 0.4962886971214773 0.7487649732129351 chrX 155270560 1976135 0.012727042396188949 0.1281560643190645 chrY 59373566 110836 0.0018667566640683162 0.052948479742080244