BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524852.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 = 926,438 number of mapped reads = 852,135 (91.98%) number of supplementary alignments = 4,178 (0.45%) number of secondary alignments = 0 number of mapped bases = 49,872,822 bp number of sequenced bases = 49,858,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,574 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8623 >>>>>>> ACTG content number of A's = 13,161,455 bp (26.4%) number of C's = 9,553,287 bp (19.16%) number of T's = 15,679,701 bp (31.45%) number of G's = 11,456,695 bp (22.98%) number of N's = 6,985 bp (0.01%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 237,943 number of insertions = 4,140 mapped reads with insertion percentage = 0.48% number of deletions = 9,357 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.24% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 0.1834X There is a 1.51% of reference with a coverageData >= 1X There is a 0.06% 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 4286136 0.01719608955357427 0.3414032267720618 chr2 243199373 3262490 0.013414878335233207 0.18113968236591985 chr3 198022430 3649900 0.018431750383024793 0.14073269851780518 chr4 191154276 2744675 0.014358428476902082 0.12844958111767257 chr5 180915260 3083890 0.01704604686193967 0.13593110678416157 chr6 171115067 3334809 0.01948869295069148 0.1553589237885336 chr7 159138663 2033367 0.012777328662111481 0.22978799933914795 chr8 146364022 5508314 0.037634344319944966 0.2556708407229183 chr9 141213431 1605413 0.011368699058094551 0.13929153336379188 chr10 135534747 2542707 0.018760554442913448 0.17772750130122794 chr11 135006516 2455562 0.01818847025131735 0.1638841196749567 chr12 133851895 2029099 0.015159284819987046 0.1302504113580052 chr13 115169878 1051652 0.009131311227055393 0.10020486866292447 chr14 107349540 1079357 0.010054602935420124 0.10786208207018397 chr15 102531392 1528236 0.014905054639265992 0.12771225682899096 chr16 90354753 1497816 0.016577058209655004 0.13979189457441063 chr17 81195210 1356258 0.01670367008103064 0.14552141047965245 chr18 78077248 1234898 0.015816361765209758 0.24988369316402587 chr19 59128983 766212 0.012958315214046553 0.2328053108521599 chr20 63025520 1087504 0.017254978618185143 0.1381446250737953 chr21 48129895 744149 0.015461263732239598 0.13227602531026528 chr22 51304566 302236 0.005891015626172532 0.07918625225177132 chrMT 16571 22144 1.336310421821254 1.3247570831049724 chrX 155270560 2545876 0.016396385766883303 0.1447910034089739 chrY 59373566 120122 0.0020231562308384845 0.05884734095024448