BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716759.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 = 1,636,156 number of mapped reads = 1,375,672 (84.08%) number of supplementary alignments = 4,071 (0.25%) number of secondary alignments = 0 number of mapped bases = 76,476,545 bp number of sequenced bases = 76,456,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,788 duplication rate = 1.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2367 >>>>>>> ACTG content number of A's = 17,552,895 bp (22.96%) number of C's = 16,644,022 bp (21.77%) number of T's = 22,156,095 bp (28.98%) number of G's = 20,101,545 bp (26.29%) number of N's = 2,038 bp (0%) GC percentage = 48.06% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 399,394 number of insertions = 5,937 mapped reads with insertion percentage = 0.43% number of deletions = 11,972 mapped reads with deletion percentage = 0.86% homopolymer indels = 35.27% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2017X There is a 2.21% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7493939 0.03006587895321633 0.2494058311512146 chr2 243199373 6974071 0.028676352714116577 0.2404107087379471 chr3 198022430 5077697 0.025642029541804934 0.18093463271750707 chr4 191154276 4740605 0.02479988990672644 0.19751059172242333 chr5 180915260 4816379 0.026622292668954516 0.17852420115605194 chr6 171115067 3512730 0.020528466964279655 0.16315814491875044 chr7 159138663 4316631 0.02712496711122928 0.23550099279103423 chr8 146364022 4732339 0.03233266574213163 0.20794038628836845 chr9 141213431 3344617 0.023684836324102912 0.1845234183069086 chr10 135534747 4005518 0.02955343990128229 0.2873526942255545 chr11 135006516 3345784 0.024782389021875063 0.20896328650851514 chr12 133851895 3890623 0.0290666262139957 0.18890802293917255 chr13 115169878 1358565 0.011796183373572732 0.12038926729215269 chr14 107349540 2305621 0.021477697994793456 0.16346976075952313 chr15 102531392 1597459 0.015580194210179064 0.14280063401244666 chr16 90354753 1804312 0.019969198521299705 0.16930075229532712 chr17 81195210 3194257 0.03934046109370245 0.2314938144354575 chr18 78077248 2032433 0.026031053246139003 0.23673081481785113 chr19 59128983 1906913 0.032250055780597475 0.24172885146651338 chr20 63025520 1547366 0.02455141980581834 0.1816209919074582 chr21 48129895 1047910 0.02177253866853439 0.1775427213915981 chr22 51304566 761405 0.014840881803775515 0.13609732304081285 chrMT 16571 8240 0.4972542393337759 0.7586972860740077 chrX 155270560 2436895 0.015694507703198857 0.14884131152667732 chrY 59373566 224236 0.0037766975289980054 0.11356399897283645