BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777270.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 55,627,034 number of mapped reads = 55,203,436 (99.24%) number of supplementary alignments = 2,011,365 (3.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,605,587 number of mapped paired reads (second in pair) = 27,597,849 number of mapped paired reads (both in pair) = 55,026,860 number of mapped paired reads (singletons) = 176,576 number of mapped bases = 5,534,172,637 bp number of sequenced bases = 5,533,341,248 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,944,161 duplication rate = 37.01% >>>>>>> Insert size mean insert size = 338,999.129 std insert size = 5,710,154.6314 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 54.5716 >>>>>>> ACTG content number of A's = 1,537,466,482 bp (27.79%) number of C's = 1,229,465,493 bp (22.22%) number of T's = 1,526,032,447 bp (27.58%) number of G's = 1,240,167,971 bp (22.41%) number of N's = 208,855 bp (0%) GC percentage = 44.63% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 13,721,859 number of insertions = 1,002,525 mapped reads with insertion percentage = 1.79% number of deletions = 368,508 mapped reads with deletion percentage = 0.66% homopolymer indels = 51.9% >>>>>>> Coverage mean coverageData = 1.7877X std coverageData = 15.9492X There is a 22.26% of reference with a coverageData >= 1X There is a 11.26% of reference with a coverageData >= 2X There is a 6.62% of reference with a coverageData >= 3X There is a 4.78% of reference with a coverageData >= 4X There is a 3.79% of reference with a coverageData >= 5X There is a 3.25% of reference with a coverageData >= 6X There is a 2.9% of reference with a coverageData >= 7X There is a 2.66% of reference with a coverageData >= 8X There is a 2.47% of reference with a coverageData >= 9X There is a 2.33% of reference with a coverageData >= 10X There is a 2.2% of reference with a coverageData >= 11X There is a 2.1% of reference with a coverageData >= 12X There is a 2.01% of reference with a coverageData >= 13X There is a 1.93% of reference with a coverageData >= 14X There is a 1.85% of reference with a coverageData >= 15X There is a 1.78% of reference with a coverageData >= 16X There is a 1.72% of reference with a coverageData >= 17X There is a 1.66% of reference with a coverageData >= 18X There is a 1.61% of reference with a coverageData >= 19X There is a 1.56% of reference with a coverageData >= 20X There is a 1.52% of reference with a coverageData >= 21X There is a 1.47% of reference with a coverageData >= 22X There is a 1.43% of reference with a coverageData >= 23X There is a 1.39% of reference with a coverageData >= 24X There is a 1.35% of reference with a coverageData >= 25X There is a 1.32% of reference with a coverageData >= 26X There is a 1.28% of reference with a coverageData >= 27X There is a 1.25% of reference with a coverageData >= 28X There is a 1.22% of reference with a coverageData >= 29X There is a 1.19% of reference with a coverageData >= 30X There is a 1.16% of reference with a coverageData >= 31X There is a 1.14% of reference with a coverageData >= 32X There is a 1.11% of reference with a coverageData >= 33X There is a 1.09% of reference with a coverageData >= 34X There is a 1.06% of reference with a coverageData >= 35X There is a 1.04% of reference with a coverageData >= 36X There is a 1.02% of reference with a coverageData >= 37X There is a 1% of reference with a coverageData >= 38X There is a 0.98% of reference with a coverageData >= 39X There is a 0.96% of reference with a coverageData >= 40X There is a 0.94% of reference with a coverageData >= 41X There is a 0.92% of reference with a coverageData >= 42X There is a 0.9% of reference with a coverageData >= 43X There is a 0.88% of reference with a coverageData >= 44X There is a 0.86% of reference with a coverageData >= 45X There is a 0.85% of reference with a coverageData >= 46X There is a 0.83% of reference with a coverageData >= 47X There is a 0.82% of reference with a coverageData >= 48X There is a 0.8% of reference with a coverageData >= 49X There is a 0.79% of reference with a coverageData >= 50X There is a 0.77% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 545379880 2.188078319772772 17.929047649920165 chr2 243199373 490626404 2.0173835069879065 16.43131499013638 chr3 198022430 343523812 1.7347722275703819 16.064104558209745 chr4 191154276 248006501 1.2974153976027196 12.386720896458558 chr5 180915260 292051270 1.6142987053717857 14.099405915598055 chr6 171115067 260191872 1.5205666956259323 13.41106739914527 chr7 159138663 367380233 2.308554226071385 19.993007870052566 chr8 146364022 189065314 1.2917471890735552 13.562536504644436 chr9 141213431 190387435 1.3482246954257489 13.023771197386157 chr10 135534747 232262567 1.7136754385205737 14.493425296500114 chr11 135006516 377310508 2.7947577582107224 22.15198618343428 chr12 133851895 316819015 2.3669370911782757 17.9309370807605 chr13 115169878 164631072 1.4294629364806655 14.418555903067212 chr14 107349540 121186164 1.128893183892544 11.255140014300297 chr15 102531392 260738387 2.5430103104422885 21.08434294303532 chr16 90354753 157945707 1.7480619641558868 14.028751615227364 chr17 81195210 234268757 2.885253415811105 21.51639818900635 chr18 78077248 86410372 1.1067292228332637 10.807408112523362 chr19 59128983 260861363 4.411734309720835 28.219929112869945 chr20 63025520 150178131 2.382814628106202 18.113798998688857 chr21 48129895 37072074 0.7702504649137506 9.623486099804579 chr22 51304566 54594710 1.0641296527096633 9.43264917306548 chrMT 16571 2324994 140.30499064630982 47.101011611634235 chrX 155270560 149102857 0.9602777049300266 10.155873860563975 chrY 59373566 1853238 0.031213183321345393 0.9303141321565799