BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163160.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 = 82,517,320 number of mapped reads = 81,422,545 (98.67%) number of supplementary alignments = 932,231 (1.13%) number of secondary alignments = 0 number of mapped bases = 8,099,575,010 bp number of sequenced bases = 8,098,268,929 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,328,885 duplication rate = 50.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2933 >>>>>>> ACTG content number of A's = 2,125,063,904 bp (26.24%) number of C's = 1,922,672,498 bp (23.74%) number of T's = 2,148,416,964 bp (26.53%) number of G's = 1,895,991,456 bp (23.41%) number of N's = 6,124,107 bp (0.08%) GC percentage = 47.15% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 55,342,174 number of insertions = 577,967 mapped reads with insertion percentage = 0.7% number of deletions = 640,349 mapped reads with deletion percentage = 0.78% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 2.6164X std coverageData = 24.6938X There is a 8.81% of reference with a coverageData >= 1X There is a 6.33% of reference with a coverageData >= 2X There is a 5.2% of reference with a coverageData >= 3X There is a 4.69% of reference with a coverageData >= 4X There is a 4.32% of reference with a coverageData >= 5X There is a 4.07% of reference with a coverageData >= 6X There is a 3.86% of reference with a coverageData >= 7X There is a 3.69% of reference with a coverageData >= 8X There is a 3.54% of reference with a coverageData >= 9X There is a 3.41% of reference with a coverageData >= 10X There is a 3.3% of reference with a coverageData >= 11X There is a 3.19% of reference with a coverageData >= 12X There is a 3.09% of reference with a coverageData >= 13X There is a 3% of reference with a coverageData >= 14X There is a 2.92% of reference with a coverageData >= 15X There is a 2.84% of reference with a coverageData >= 16X There is a 2.76% of reference with a coverageData >= 17X There is a 2.69% of reference with a coverageData >= 18X There is a 2.63% of reference with a coverageData >= 19X There is a 2.57% of reference with a coverageData >= 20X There is a 2.5% of reference with a coverageData >= 21X There is a 2.45% of reference with a coverageData >= 22X There is a 2.39% of reference with a coverageData >= 23X There is a 2.34% of reference with a coverageData >= 24X There is a 2.29% of reference with a coverageData >= 25X There is a 2.24% of reference with a coverageData >= 26X There is a 2.19% of reference with a coverageData >= 27X There is a 2.15% of reference with a coverageData >= 28X There is a 2.1% of reference with a coverageData >= 29X There is a 2.06% of reference with a coverageData >= 30X There is a 2.02% of reference with a coverageData >= 31X There is a 1.98% of reference with a coverageData >= 32X There is a 1.94% of reference with a coverageData >= 33X There is a 1.91% of reference with a coverageData >= 34X There is a 1.87% of reference with a coverageData >= 35X There is a 1.83% of reference with a coverageData >= 36X There is a 1.8% of reference with a coverageData >= 37X There is a 1.77% of reference with a coverageData >= 38X There is a 1.73% of reference with a coverageData >= 39X There is a 1.7% of reference with a coverageData >= 40X There is a 1.67% of reference with a coverageData >= 41X There is a 1.64% of reference with a coverageData >= 42X There is a 1.62% of reference with a coverageData >= 43X There is a 1.59% of reference with a coverageData >= 44X There is a 1.56% of reference with a coverageData >= 45X There is a 1.53% of reference with a coverageData >= 46X There is a 1.51% of reference with a coverageData >= 47X There is a 1.48% of reference with a coverageData >= 48X There is a 1.46% of reference with a coverageData >= 49X There is a 1.43% of reference with a coverageData >= 50X There is a 1.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 938645019 3.765868326562765 30.745741087065554 chr2 243199373 554176843 2.278693551566023 20.621091147982813 chr3 198022430 403698577 2.0386507578964665 17.394439642398233 chr4 191154276 319847724 1.6732438880938243 19.261878661000683 chr5 180915260 388232745 2.1459369707121443 28.175652038265323 chr6 171115067 393676796 2.300655359589112 20.409464768764895 chr7 159138663 430309341 2.7039899222981405 24.456157094233877 chr8 146364022 362635811 2.4776294477614176 38.96719306778119 chr9 141213431 337069696 2.3869521023110045 20.918652756530562 chr10 135534747 332141597 2.4506010772278195 20.489550329876863 chr11 135006516 389012795 2.88143718189128 21.549981284916054 chr12 133851895 392297651 2.9308337472547548 22.60699210592899 chr13 115169878 151902548 1.3189433785802915 15.558952922934155 chr14 107349540 219144133 2.0414072850242304 17.307211051373947 chr15 102531392 341788605 3.3335020458904916 25.95490195260887 chr16 90354753 290807677 3.2185100102038904 23.125844058808223 chr17 81195210 415765507 5.120566927531809 34.671272317275495 chr18 78077248 123879899 1.5866324976003252 15.576270558397333 chr19 59128983 479783427 8.114183648313382 46.89391513155793 chr20 63025520 171876374 2.7270917241142953 21.716016058866593 chr21 48129895 105554710 2.1931215515845195 34.14963735263197 chr22 51304566 160474343 3.127876435013601 24.750440897764346 chrMT 16571 7899 0.4766761209341621 1.0414060219258119 chrX 155270560 387283527 2.494249566691844 22.731199056204733 chrY 59373566 9561766 0.16104415894440297 13.258494016306766