BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163070.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 92,258,792 number of mapped reads = 90,975,423 (98.61%) number of supplementary alignments = 617,375 (0.67%) number of secondary alignments = 0 number of mapped bases = 8,906,513,652 bp number of sequenced bases = 8,905,337,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,362,443 duplication rate = 45.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.95 >>>>>>> ACTG content number of A's = 2,174,720,458 bp (24.42%) number of C's = 2,278,506,963 bp (25.59%) number of T's = 2,158,129,699 bp (24.23%) number of G's = 2,293,336,411 bp (25.75%) number of N's = 643,491 bp (0.01%) GC percentage = 51.34% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 33,387,482 number of insertions = 605,686 mapped reads with insertion percentage = 0.66% number of deletions = 534,185 mapped reads with deletion percentage = 0.58% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 2.8771X std coverageData = 37.1961X There is a 12.44% of reference with a coverageData >= 1X There is a 7.52% of reference with a coverageData >= 2X There is a 5.13% of reference with a coverageData >= 3X There is a 4.43% of reference with a coverageData >= 4X There is a 3.93% of reference with a coverageData >= 5X There is a 3.65% of reference with a coverageData >= 6X There is a 3.42% of reference with a coverageData >= 7X There is a 3.24% of reference with a coverageData >= 8X There is a 3.09% of reference with a coverageData >= 9X There is a 2.97% of reference with a coverageData >= 10X There is a 2.85% of reference with a coverageData >= 11X There is a 2.75% of reference with a coverageData >= 12X There is a 2.66% of reference with a coverageData >= 13X There is a 2.57% of reference with a coverageData >= 14X There is a 2.49% of reference with a coverageData >= 15X There is a 2.42% of reference with a coverageData >= 16X There is a 2.35% of reference with a coverageData >= 17X There is a 2.29% of reference with a coverageData >= 18X There is a 2.23% of reference with a coverageData >= 19X There is a 2.17% of reference with a coverageData >= 20X There is a 2.12% of reference with a coverageData >= 21X There is a 2.07% of reference with a coverageData >= 22X There is a 2.02% of reference with a coverageData >= 23X There is a 1.97% of reference with a coverageData >= 24X There is a 1.93% of reference with a coverageData >= 25X There is a 1.89% of reference with a coverageData >= 26X There is a 1.85% of reference with a coverageData >= 27X There is a 1.81% of reference with a coverageData >= 28X There is a 1.77% of reference with a coverageData >= 29X There is a 1.74% of reference with a coverageData >= 30X There is a 1.7% of reference with a coverageData >= 31X There is a 1.67% of reference with a coverageData >= 32X There is a 1.64% of reference with a coverageData >= 33X There is a 1.61% of reference with a coverageData >= 34X There is a 1.58% of reference with a coverageData >= 35X There is a 1.55% of reference with a coverageData >= 36X There is a 1.53% of reference with a coverageData >= 37X There is a 1.5% of reference with a coverageData >= 38X There is a 1.47% of reference with a coverageData >= 39X There is a 1.45% of reference with a coverageData >= 40X There is a 1.42% of reference with a coverageData >= 41X There is a 1.4% of reference with a coverageData >= 42X There is a 1.38% of reference with a coverageData >= 43X There is a 1.36% of reference with a coverageData >= 44X There is a 1.33% of reference with a coverageData >= 45X There is a 1.31% of reference with a coverageData >= 46X There is a 1.29% of reference with a coverageData >= 47X There is a 1.27% of reference with a coverageData >= 48X There is a 1.25% of reference with a coverageData >= 49X There is a 1.23% of reference with a coverageData >= 50X There is a 1.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1274282549 5.112454861245863 50.92174453281801 chr2 243199373 383355601 1.576301765383252 19.497823354490485 chr3 198022430 386982912 1.9542377699334363 21.976436058671577 chr4 191154276 184903951 0.9673021962637132 15.160786224873647 chr5 180915260 500296302 2.7653626454728033 48.61726788093398 chr6 171115067 507061788 2.963279604127438 33.93076165017628 chr7 159138663 591361724 3.7160154097813427 61.872231737451315 chr8 146364022 421940498 2.882815682668245 47.26496094211163 chr9 141213431 428070168 3.0313700684745775 35.28230138255998 chr10 135534747 197398388 1.4564411884725028 16.236886152104958 chr11 135006516 505611224 3.7450875630328837 34.39074063662037 chr12 133851895 225837637 1.6872203191445292 20.036969475189952 chr13 115169878 126567870 1.0989667801853538 15.077019309368115 chr14 107349540 248362925 2.313590957166654 23.31543876556277 chr15 102531392 465774083 4.54274611818398 45.50484687204857 chr16 90354753 392394332 4.342818932834668 37.2322880518045 chr17 81195210 229830272 2.8305890458316445 26.08412961733405 chr18 78077248 148439792 1.901191394450788 20.02776848921996 chr19 59128983 727287732 12.30002098970652 87.02644082152527 chr20 63025520 219956062 3.4899523558076155 31.77407543061811 chr21 48129895 117293232 2.4370140844894843 44.664410411473014 chr22 51304566 107411674 2.0936084714175345 25.47289650978058 chrMT 16571 242 0.014603825961016233 0.11996063616168673 chrX 155270560 503757626 3.2443859673076467 40.44372340094957 chrY 59373566 12335068 0.20775353126002236 9.770419623969739