BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153398.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 = 49,028,572 number of mapped reads = 48,434,634 (98.79%) number of supplementary alignments = 386,746 (0.79%) number of secondary alignments = 0 number of mapped bases = 4,561,404,487 bp number of sequenced bases = 4,560,505,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,161,582 duplication rate = 32.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.1131 >>>>>>> ACTG content number of A's = 1,215,394,501 bp (26.65%) number of C's = 1,063,317,556 bp (23.32%) number of T's = 1,241,701,414 bp (27.23%) number of G's = 1,038,192,474 bp (22.76%) number of N's = 1,900,053 bp (0.04%) GC percentage = 46.08% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 14,349,749 number of insertions = 505,199 mapped reads with insertion percentage = 1.03% number of deletions = 421,045 mapped reads with deletion percentage = 0.86% homopolymer indels = 49.39% >>>>>>> Coverage mean coverageData = 1.4735X std coverageData = 12.2783X There is a 24.85% of reference with a coverageData >= 1X There is a 13.72% of reference with a coverageData >= 2X There is a 7.21% of reference with a coverageData >= 3X There is a 5.12% of reference with a coverageData >= 4X There is a 3.82% of reference with a coverageData >= 5X There is a 3.2% of reference with a coverageData >= 6X There is a 2.79% of reference with a coverageData >= 7X There is a 2.52% of reference with a coverageData >= 8X There is a 2.31% of reference with a coverageData >= 9X There is a 2.15% of reference with a coverageData >= 10X There is a 2.01% of reference with a coverageData >= 11X There is a 1.9% of reference with a coverageData >= 12X There is a 1.8% of reference with a coverageData >= 13X There is a 1.71% of reference with a coverageData >= 14X There is a 1.63% of reference with a coverageData >= 15X There is a 1.56% of reference with a coverageData >= 16X There is a 1.49% of reference with a coverageData >= 17X There is a 1.43% of reference with a coverageData >= 18X There is a 1.37% of reference with a coverageData >= 19X There is a 1.32% of reference with a coverageData >= 20X There is a 1.27% of reference with a coverageData >= 21X There is a 1.23% of reference with a coverageData >= 22X There is a 1.18% of reference with a coverageData >= 23X There is a 1.14% of reference with a coverageData >= 24X There is a 1.1% of reference with a coverageData >= 25X There is a 1.07% of reference with a coverageData >= 26X There is a 1.03% of reference with a coverageData >= 27X There is a 1% of reference with a coverageData >= 28X There is a 0.97% of reference with a coverageData >= 29X There is a 0.94% of reference with a coverageData >= 30X There is a 0.92% of reference with a coverageData >= 31X There is a 0.89% of reference with a coverageData >= 32X There is a 0.86% of reference with a coverageData >= 33X There is a 0.84% of reference with a coverageData >= 34X There is a 0.82% of reference with a coverageData >= 35X There is a 0.79% of reference with a coverageData >= 36X There is a 0.77% of reference with a coverageData >= 37X There is a 0.75% of reference with a coverageData >= 38X There is a 0.73% of reference with a coverageData >= 39X There is a 0.72% of reference with a coverageData >= 40X There is a 0.7% of reference with a coverageData >= 41X There is a 0.68% of reference with a coverageData >= 42X There is a 0.66% of reference with a coverageData >= 43X There is a 0.65% of reference with a coverageData >= 44X There is a 0.63% of reference with a coverageData >= 45X There is a 0.62% of reference with a coverageData >= 46X There is a 0.6% of reference with a coverageData >= 47X There is a 0.59% of reference with a coverageData >= 48X There is a 0.58% of reference with a coverageData >= 49X There is a 0.56% of reference with a coverageData >= 50X There is a 0.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 475571842 1.9080066484568559 16.495159794915555 chr2 243199373 333757661 1.3723623415756092 10.504331489527624 chr3 198022430 263994773 1.3331559106713315 10.161352816981431 chr4 191154276 204231955 1.0684142634612055 9.093293486347706 chr5 180915260 231994485 1.2823378470119104 10.619657742729055 chr6 171115067 249131248 1.4559281796032608 11.620940695772854 chr7 159138663 240629266 1.5120729398109873 12.44194981602523 chr8 146364022 195721266 1.3372225177031551 15.47671048713157 chr9 141213431 188478756 1.3347084244415817 10.912377128380308 chr10 135534747 189252681 1.3963406815523107 9.991158667771845 chr11 135006516 232779156 1.7242068227284675 12.099328788273304 chr12 133851895 242291202 1.8101439804046107 14.208262857236308 chr13 115169878 90989773 0.7900483579569304 6.858009594129437 chr14 107349540 139898646 1.3032067580354791 10.178351166029472 chr15 102531392 171740828 1.675007279721707 13.315301754791127 chr16 90354753 170947127 1.8919550031861634 14.450962186291227 chr17 81195210 195655209 2.409689056780566 15.534914781327132 chr18 78077248 83768647 1.0728944621613712 8.555808528709695 chr19 59128983 186855542 3.16013454856817 18.836472348325916 chr20 63025520 91536605 1.4523736575279347 11.065365066492932 chr21 48129895 41856566 0.8696583692941777 7.8112541236916035 chr22 51304566 72592908 1.4149404947699977 11.714528341998497 chrMT 16571 53484 3.2275662301611248 7.738529866067599 chrX 155270560 264383669 1.7027288946468668 15.431655694633955 chrY 59373566 3291192 0.05543194087415938 2.3046713107292063