BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975301.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 67,987,954 number of mapped reads = 67,889,933 (99.86%) number of supplementary alignments = 105,273 (0.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 33,954,362 number of mapped paired reads (second in pair) = 33,935,571 number of mapped paired reads (both in pair) = 67,842,456 number of mapped paired reads (singletons) = 47,477 number of mapped bases = 6,361,241,601 bp number of sequenced bases = 6,359,293,896 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,712,617 duplication rate = 48.81% >>>>>>> Insert size mean insert size = 67,613.805 std insert size = 2,566,028.4881 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 56.0846 >>>>>>> ACTG content number of A's = 1,690,525,816 bp (26.58%) number of C's = 1,422,094,274 bp (22.36%) number of T's = 1,741,433,682 bp (27.38%) number of G's = 1,504,961,146 bp (23.67%) number of N's = 278,978 bp (0%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 37,731,447 number of insertions = 511,682 mapped reads with insertion percentage = 0.75% number of deletions = 1,380,550 mapped reads with deletion percentage = 2.01% homopolymer indels = 48.44% >>>>>>> Coverage mean coverageData = 2.0549X std coverageData = 26.9959X There is a 11% of reference with a coverageData >= 1X There is a 5.71% of reference with a coverageData >= 2X There is a 3.59% of reference with a coverageData >= 3X There is a 2.88% of reference with a coverageData >= 4X There is a 2.45% of reference with a coverageData >= 5X There is a 2.23% of reference with a coverageData >= 6X There is a 2.06% of reference with a coverageData >= 7X There is a 1.95% of reference with a coverageData >= 8X There is a 1.86% of reference with a coverageData >= 9X There is a 1.78% of reference with a coverageData >= 10X There is a 1.72% of reference with a coverageData >= 11X There is a 1.66% of reference with a coverageData >= 12X There is a 1.61% of reference with a coverageData >= 13X There is a 1.56% of reference with a coverageData >= 14X There is a 1.52% of reference with a coverageData >= 15X There is a 1.48% of reference with a coverageData >= 16X There is a 1.45% of reference with a coverageData >= 17X There is a 1.41% of reference with a coverageData >= 18X There is a 1.38% of reference with a coverageData >= 19X There is a 1.35% of reference with a coverageData >= 20X There is a 1.32% of reference with a coverageData >= 21X There is a 1.3% of reference with a coverageData >= 22X There is a 1.27% of reference with a coverageData >= 23X There is a 1.25% of reference with a coverageData >= 24X There is a 1.23% of reference with a coverageData >= 25X There is a 1.2% of reference with a coverageData >= 26X There is a 1.18% of reference with a coverageData >= 27X There is a 1.16% of reference with a coverageData >= 28X There is a 1.14% of reference with a coverageData >= 29X There is a 1.12% of reference with a coverageData >= 30X There is a 1.11% of reference with a coverageData >= 31X There is a 1.09% of reference with a coverageData >= 32X There is a 1.07% of reference with a coverageData >= 33X There is a 1.05% of reference with a coverageData >= 34X There is a 1.04% of reference with a coverageData >= 35X There is a 1.02% of reference with a coverageData >= 36X There is a 1.01% of reference with a coverageData >= 37X There is a 0.99% of reference with a coverageData >= 38X There is a 0.98% of reference with a coverageData >= 39X There is a 0.97% of reference with a coverageData >= 40X There is a 0.95% of reference with a coverageData >= 41X There is a 0.94% of reference with a coverageData >= 42X There is a 0.93% of reference with a coverageData >= 43X There is a 0.91% of reference with a coverageData >= 44X There is a 0.9% of reference with a coverageData >= 45X There is a 0.89% of reference with a coverageData >= 46X There is a 0.88% of reference with a coverageData >= 47X There is a 0.87% of reference with a coverageData >= 48X There is a 0.86% of reference with a coverageData >= 49X There is a 0.85% of reference with a coverageData >= 50X There is a 0.84% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 775294004 3.1104997888851798 36.19010532542365 chr2 243199373 473626489 1.9474823604911184 23.693945988458786 chr3 198022430 324621063 1.639314611986127 21.41826651642073 chr4 191154276 286394015 1.4982349387779323 21.981334892479943 chr5 180915260 308819960 1.7069867959176026 22.635095799766123 chr6 171115067 588767364 3.4407686846185204 46.08223655173587 chr7 159138663 338910051 2.129652496829133 29.121484959389022 chr8 146364022 218480099 1.492717240306501 20.348932167799582 chr9 141213431 259580065 1.8382108781139948 23.538114703422 chr10 135534747 279197126 2.059967146284635 26.477239362814736 chr11 135006516 296578801 2.196773976450144 24.919717319543157 chr12 133851895 358553907 2.678736128464972 28.29600493976494 chr13 115169878 128757675 1.1179804757629421 20.090150807028635 chr14 107349540 208505773 1.9423070932581545 24.744503453698933 chr15 102531392 244769407 2.3872630832906276 27.75916613284859 chr16 90354753 194942818 2.1575269869865066 25.488505429827537 chr17 81195210 246712994 3.038516607075713 29.62127746093693 chr18 78077248 119501709 1.5305573910596848 25.79916588418811 chr19 59128983 235445828 3.981902208600476 35.62168345315708 chr20 63025520 158132814 2.5090283110714515 30.700856985617655 chr21 48129895 34178260 0.7101253804937658 12.222221981840702 chr22 51304566 113592013 2.2140721938862127 26.064735585224856 chrMT 16571 80287 4.845030474926076 13.000286222068816 chrX 155270560 166208917 1.0704470763807383 16.536358575522925 chrY 59373566 1590162 0.02678232262485295 1.6361159741394853