BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240231.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 = 3,233,003 number of mapped reads = 2,542,580 (78.64%) number of supplementary alignments = 19,585 (0.61%) number of secondary alignments = 0 number of mapped bases = 163,144,038 bp number of sequenced bases = 163,066,789 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 485,427 duplication rate = 13.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4273 >>>>>>> ACTG content number of A's = 45,190,937 bp (27.71%) number of C's = 29,278,052 bp (17.95%) number of T's = 52,443,810 bp (32.16%) number of G's = 36,094,452 bp (22.13%) number of N's = 59,538 bp (0.04%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,445,090 number of insertions = 11,557 mapped reads with insertion percentage = 0.45% number of deletions = 45,312 mapped reads with deletion percentage = 1.76% homopolymer indels = 47.85% >>>>>>> Coverage mean coverageData = 0.0527X std coverageData = 0.5659X There is a 2.27% of reference with a coverageData >= 1X There is a 1.13% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 13055682 0.052379737100033144 0.7692980266840478 chr2 243199373 17285203 0.07107420873161543 0.7138734936908819 chr3 198022430 10675447 0.05391029187956132 0.46422669483047024 chr4 191154276 10735993 0.05616402219534969 0.48942589891356003 chr5 180915260 8444670 0.04667748867619017 0.43046459575440077 chr6 171115067 8509918 0.04973213726410194 0.487796428163782 chr7 159138663 9681866 0.06083918148790781 0.7582985842763851 chr8 146364022 9277660 0.06338757211796216 0.7592502931526205 chr9 141213431 6158779 0.0436132665029575 0.49412763081002675 chr10 135534747 7745063 0.05714448266170446 0.5612483103783482 chr11 135006516 7108784 0.05265511777224145 0.5419811416554856 chr12 133851895 8262080 0.061725536272758785 0.5015686868137372 chr13 115169878 4199314 0.03646191237608153 0.3885218459956043 chr14 107349540 5398657 0.050290453037805286 0.4710274380398695 chr15 102531392 4679848 0.04564307485457722 0.4658224922077192 chr16 90354753 4752744 0.0526009295825312 0.46047479192411694 chr17 81195210 3854297 0.047469512056191494 0.4421012300938683 chr18 78077248 3867197 0.04953039584591916 0.7525309787500478 chr19 59128983 2885134 0.048793905350951156 0.5700855430080122 chr20 63025520 3346344 0.05309506371387336 0.4548727033125265 chr21 48129895 2540552 0.052785321887778895 0.4603736267362871 chr22 51304566 1507685 0.029386955539200937 0.32667753067451566 chrMT 16571 30902 1.864824090278197 2.9455157768342923 chrX 155270560 8703863 0.05605610619295764 0.49440034109698655 chrY 59373566 436356 0.007349331182162783 0.16889692580006765