BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751171.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,551,272 number of mapped reads = 4,350,934 (95.6%) number of supplementary alignments = 149,818 (3.29%) number of secondary alignments = 0 number of mapped bases = 428,478,661 bp number of sequenced bases = 428,351,155 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,254 duplication rate = 1.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.3335 >>>>>>> ACTG content number of A's = 124,197,620 bp (28.99%) number of C's = 90,005,782 bp (21.01%) number of T's = 124,889,931 bp (29.16%) number of G's = 89,255,451 bp (20.84%) number of N's = 2,371 bp (0%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,478,201 number of insertions = 157,036 mapped reads with insertion percentage = 3.52% number of deletions = 58,019 mapped reads with deletion percentage = 1.31% homopolymer indels = 51.08% >>>>>>> Coverage mean coverageData = 0.1384X std coverageData = 0.9709X There is a 11.22% of reference with a coverageData >= 1X There is a 1.93% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 53846444 0.21603333939135902 2.640908521964031 chr2 243199373 32947845 0.13547668562451434 0.4998291581364772 chr3 198022430 28752943 0.14520043512242528 0.4455551081937798 chr4 191154276 18199988 0.09521099072876613 0.3948016274247145 chr5 180915260 27513014 0.15207680103933743 0.44261810385438194 chr6 171115067 24444447 0.1428538551780481 0.7089834152064216 chr7 159138663 23358476 0.1467806475161853 0.6487492739421263 chr8 146364022 20594414 0.14070680566567104 0.46939085392376145 chr9 141213431 19180214 0.13582428997139798 0.5543045727847762 chr10 135534747 21954213 0.16198217420954053 1.2834290885844657 chr11 135006516 19614634 0.1452865726866102 0.5571093366256358 chr12 133851895 23455841 0.17523727250929097 0.4784142995754291 chr13 115169878 11692872 0.10152717188777434 0.360495544268452 chr14 107349540 9517798 0.08866174927251667 0.3479866901808249 chr15 102531392 11800457 0.1150911615439689 0.3861758968021231 chr16 90354753 12269241 0.13578965790543415 0.6287633790420183 chr17 81195210 14091656 0.1735527994816443 0.619429640624748 chr18 78077248 8295033 0.10624135983891235 0.872251965415065 chr19 59128983 8968235 0.15167240403914947 1.783261717756641 chr20 63025520 8397534 0.1332402176134366 0.4213375958556976 chr21 48129895 5133016 0.10664922497753215 0.3981945779636845 chr22 51304566 5686494 0.11083797102971303 0.3854378678557261 chrMT 16571 977673 58.9990344577877 23.290432466421926 chrX 155270560 17009482 0.10954737330759932 0.40407735923924637 chrY 59373566 776697 0.013081528571148986 0.4160232444186457