BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236126.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 807,903 number of mapped reads = 692,857 (85.76%) number of supplementary alignments = 3,778 (0.47%) number of secondary alignments = 0 number of mapped bases = 44,801,572 bp number of sequenced bases = 44,776,991 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,025 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.24 >>>>>>> ACTG content number of A's = 12,063,483 bp (26.94%) number of C's = 7,971,395 bp (17.8%) number of T's = 14,403,096 bp (32.17%) number of G's = 10,316,335 bp (23.04%) number of N's = 22,682 bp (0.05%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 379,995 number of insertions = 3,180 mapped reads with insertion percentage = 0.46% number of deletions = 14,012 mapped reads with deletion percentage = 2% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.1667X There is a 1.32% of reference with a coverageData >= 1X There is a 0.09% 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 1515688 0.006080979834349139 0.22795196892557532 chr2 243199373 3136832 0.012898191147885896 0.17135738555810406 chr3 198022430 2841565 0.014349712807786472 0.12708480834457575 chr4 191154276 2617353 0.013692359149737252 0.13095187734828956 chr5 180915260 2687785 0.01485659639767259 0.13052953647696813 chr6 171115067 6484230 0.037893974584949905 0.28840819895665815 chr7 159138663 1671267 0.010501954512461878 0.11818981558182723 chr8 146364022 3578480 0.024449177817756334 0.26758955205312507 chr9 141213431 2062481 0.014605416675981763 0.15352699956370824 chr10 135534747 1294498 0.009551041549514975 0.12588415381295565 chr11 135006516 1538099 0.011392776034602656 0.12819780386113558 chr12 133851895 1080826 0.008074790424147524 0.09832898029988553 chr13 115169878 2552301 0.022161185236299372 0.15886715299979082 chr14 107349540 2140328 0.0199379335952441 0.15321394885806397 chr15 102531392 1594355 0.015549920555062786 0.13623471875933063 chr16 90354753 1352205 0.01496551044746921 0.13584346234132313 chr17 81195210 696890 0.00858289546883369 0.10799217017988981 chr18 78077248 1163343 0.014899897598849795 0.2086695580748892 chr19 59128983 1248416 0.02111343602848708 0.2067971664156688 chr20 63025520 727597 0.011544482298599043 0.11582660000881269 chr21 48129895 980013 0.02036183540396255 0.157483922540954 chr22 51304566 275084 0.005361783978447454 0.07709475900239676 chrMT 16571 19592 1.1823064389596283 1.3044425246005384 chrX 155270560 1441407 0.009283195732661748 0.10761050892943931 chrY 59373566 100937 0.0017000326374198241 0.0604567807160164