BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124799.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 692,436 number of mapped reads = 691,702 (99.89%) number of supplementary alignments = 298,700 (43.14%) number of secondary alignments = 0 number of mapped bases = 102,991,401 bp number of sequenced bases = 102,946,285 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 988,359 duplication rate = 20.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.511 >>>>>>> ACTG content number of A's = 32,564,398 bp (31.63%) number of C's = 20,297,796 bp (19.72%) number of T's = 31,330,550 bp (30.43%) number of G's = 18,753,541 bp (18.22%) number of N's = 0 bp (0%) GC percentage = 37.93% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 763,679 number of insertions = 5,180 mapped reads with insertion percentage = 0.75% number of deletions = 44,509 mapped reads with deletion percentage = 6.35% homopolymer indels = 73.02% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 76.4283X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 160235 6.42867004130754E-4 0.52715947600088 chr2 243199373 33589 1.381130205463153E-4 0.1050866905774762 chr3 198022430 36991 1.8680207085631663E-4 0.15539845228597687 chr4 191154276 9250 4.8390233237576126E-5 0.007152658543560756 chr5 180915260 10265 5.6739271192490895E-5 0.007531233058419439 chr6 171115067 8491 4.9621580079795076E-5 0.02218818106526371 chr7 159138663 22942 1.4416358393057506E-4 0.12548993464876831 chr8 146364022 185815 0.0012695401332986052 0.5958984459313936 chr9 141213431 5662 4.0095336257356427E-5 0.006468057865324456 chr10 135534747 102425265 0.7557122233754566 365.26285748317935 chr11 135006516 6893 5.105679491795789E-5 0.01256497764433919 chr12 133851895 7018 5.243108437127468E-5 0.026107352942178384 chr13 115169878 3955 3.434057644829666E-5 0.005857759852062465 chr14 107349540 31098 2.8968917798809387E-4 0.36918188595417734 chr15 102531392 4752 4.6346781286262065E-5 0.007195631781642136 chr16 90354753 6202 6.864055065260375E-5 0.008403389624248195 chr17 81195210 4076 5.020000564072684E-5 0.007234671323421295 chr18 78077248 2347 3.0059973425292857E-5 0.00548261523575114 chr19 59128983 3186 5.3882205279938606E-5 0.007336795684471148 chr20 63025520 4857 7.706402105052049E-5 0.00911522850856685 chr21 48129895 2372 4.92832988727692E-5 0.009464021117442217 chr22 51304566 2547 4.964470413802935E-5 0.0073887120626945834 chrMT 16571 426 0.025707561402450063 0.1582614377831483 chrX 155270560 9741 6.273565317211453E-5 0.0228242150268223 chrY 59373566 3426 5.770244623676469E-5 0.0076677178769308345