BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975281.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 = 30,482,636 number of mapped reads = 30,331,599 (99.5%) number of supplementary alignments = 58,725 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,207,334 number of mapped paired reads (second in pair) = 15,124,265 number of mapped paired reads (both in pair) = 30,211,672 number of mapped paired reads (singletons) = 119,927 number of mapped bases = 2,880,610,066 bp number of sequenced bases = 2,879,690,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,047,292 duplication rate = 56.63% >>>>>>> Insert size mean insert size = 104,843.1122 std insert size = 3,168,232.7538 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 56.1868 >>>>>>> ACTG content number of A's = 798,162,514 bp (27.72%) number of C's = 614,886,898 bp (21.35%) number of T's = 830,968,643 bp (28.86%) number of G's = 635,079,151 bp (22.05%) number of N's = 592,998 bp (0.02%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 20,454,722 number of insertions = 255,880 mapped reads with insertion percentage = 0.83% number of deletions = 584,004 mapped reads with deletion percentage = 1.9% homopolymer indels = 48.14% >>>>>>> Coverage mean coverageData = 0.9305X std coverageData = 13.9505X There is a 6.35% of reference with a coverageData >= 1X There is a 4.19% of reference with a coverageData >= 2X There is a 2.59% of reference with a coverageData >= 3X There is a 2.16% of reference with a coverageData >= 4X There is a 1.86% of reference with a coverageData >= 5X There is a 1.7% of reference with a coverageData >= 6X There is a 1.57% of reference with a coverageData >= 7X There is a 1.47% of reference with a coverageData >= 8X There is a 1.39% of reference with a coverageData >= 9X There is a 1.32% of reference with a coverageData >= 10X There is a 1.25% of reference with a coverageData >= 11X There is a 1.2% of reference with a coverageData >= 12X There is a 1.15% of reference with a coverageData >= 13X There is a 1.1% of reference with a coverageData >= 14X There is a 1.06% of reference with a coverageData >= 15X There is a 1.02% of reference with a coverageData >= 16X There is a 0.98% of reference with a coverageData >= 17X There is a 0.95% of reference with a coverageData >= 18X There is a 0.92% of reference with a coverageData >= 19X There is a 0.89% of reference with a coverageData >= 20X There is a 0.86% of reference with a coverageData >= 21X There is a 0.83% of reference with a coverageData >= 22X There is a 0.81% of reference with a coverageData >= 23X There is a 0.78% of reference with a coverageData >= 24X There is a 0.76% of reference with a coverageData >= 25X There is a 0.74% of reference with a coverageData >= 26X There is a 0.72% of reference with a coverageData >= 27X There is a 0.7% of reference with a coverageData >= 28X There is a 0.68% of reference with a coverageData >= 29X There is a 0.67% of reference with a coverageData >= 30X There is a 0.65% of reference with a coverageData >= 31X There is a 0.63% of reference with a coverageData >= 32X There is a 0.62% of reference with a coverageData >= 33X There is a 0.6% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.58% of reference with a coverageData >= 36X There is a 0.56% of reference with a coverageData >= 37X There is a 0.55% of reference with a coverageData >= 38X There is a 0.54% of reference with a coverageData >= 39X There is a 0.53% of reference with a coverageData >= 40X There is a 0.52% of reference with a coverageData >= 41X There is a 0.5% of reference with a coverageData >= 42X There is a 0.49% of reference with a coverageData >= 43X There is a 0.48% of reference with a coverageData >= 44X There is a 0.48% of reference with a coverageData >= 45X There is a 0.47% of reference with a coverageData >= 46X There is a 0.46% of reference with a coverageData >= 47X There is a 0.45% of reference with a coverageData >= 48X There is a 0.44% of reference with a coverageData >= 49X There is a 0.43% of reference with a coverageData >= 50X There is a 0.42% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 311683591 1.2504827059187147 16.117683982498654 chr2 243199373 245451185 1.0092591192659037 14.011166808722663 chr3 198022430 204188343 1.0311374474093666 14.925177311466108 chr4 191154276 145558427 0.7614709440242917 11.630527767837942 chr5 180915260 152752784 0.8443333304222098 12.891365360810148 chr6 171115067 237826514 1.3898630796784248 21.46221869834332 chr7 159138663 149832324 0.9415205656214417 14.133549832240185 chr8 146364022 110021717 0.7516991914857327 11.566050754666794 chr9 141213431 115063604 0.8148205392729251 11.841757686577314 chr10 135534747 126885548 0.9361846375822725 13.824082697640824 chr11 135006516 138560095 1.026321536954557 13.666163854978077 chr12 133851895 161111975 1.203658528704431 14.598372885765363 chr13 115169878 65982353 0.5729132838015162 10.6110354363758 chr14 107349540 92367745 0.860439131830467 12.383708553230175 chr15 102531392 104309368 1.0173407964655352 15.843014052018566 chr16 90354753 72517300 0.8025842315124253 10.358357612568248 chr17 81195210 96146554 1.184140714704722 14.988815591851502 chr18 78077248 57492195 0.736350172075737 12.831213528222419 chr19 59128983 91356398 1.5450358413910146 22.66670558137745 chr20 63025520 58330660 0.9255085876324384 14.888656600901834 chr21 48129895 27374452 0.5687619306046688 9.534881379169 chr22 51304566 34794057 0.6781863625939258 9.81466456434824 chrMT 16571 29290 1.7675457123891136 6.118548969092575 chrX 155270560 74257015 0.47824272031993703 8.024347172296588 chrY 59373566 6716572 0.11312394475346149 2.805547188782366