BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231888.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 = 3,999,144 number of mapped reads = 3,755,579 (93.91%) number of supplementary alignments = 41,665 (1.04%) number of secondary alignments = 0 number of mapped bases = 260,562,437 bp number of sequenced bases = 260,474,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 829,859 duplication rate = 9.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9038 >>>>>>> ACTG content number of A's = 64,725,515 bp (24.85%) number of C's = 45,713,926 bp (17.55%) number of T's = 70,415,415 bp (27.03%) number of G's = 79,563,946 bp (30.55%) number of N's = 56,031 bp (0.02%) GC percentage = 48.1% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,539,506 number of insertions = 16,234 mapped reads with insertion percentage = 0.43% number of deletions = 52,676 mapped reads with deletion percentage = 1.39% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0842X std coverageData = 56.1009X There is a 2.98% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% 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 23152752 0.09288944559941538 0.8444913403608192 chr2 243199373 31970280 0.131457082333843 200.14070338774889 chr3 198022430 4473964 0.022593218354102614 0.29561446504335015 chr4 191154276 3288500 0.01720338183802909 0.25767050460544094 chr5 180915260 21544273 0.11908488537672278 0.7111429157668725 chr6 171115067 15256290 0.08915807513315002 0.606155034179751 chr7 159138663 1886090 0.011851865313208016 0.3505774000391575 chr8 146364022 16219045 0.11081305896335644 0.8164528181093832 chr9 141213431 10982277 0.07777076813607058 0.9589621120859478 chr10 135534747 29934891 0.22086506716982324 1.066771289561941 chr11 135006516 9838671 0.07287552698567527 0.6986192774489919 chr12 133851895 15056070 0.11248305449840662 0.7269300265501917 chr13 115169878 16010551 0.13901682695192227 0.7540219459113738 chr14 107349540 2410079 0.022450762248259284 0.569300070030791 chr15 102531392 10836330 0.10568792433833338 0.6559390685066522 chr16 90354753 9569123 0.1059061386621244 0.7178302032171134 chr17 81195210 1047781 0.012904468133033956 0.22982347287155258 chr18 78077248 12245217 0.15683463894629074 1.4808482239259133 chr19 59128983 1185702 0.020052805575905136 0.8932715164260815 chr20 63025520 9566109 0.15178151643968982 0.8008941484982638 chr21 48129895 569985 0.011842639590217266 0.38585498964843035 chr22 51304566 6711407 0.13081500387314454 0.7480980374738673 chrMT 16571 10304 0.6218091847202944 1.8287650978507177 chrX 155270560 6301257 0.04058243236837685 0.46684653413671146 chrY 59373566 495489 0.00834527944641223 0.18906420804029406