BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104293.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 28,983,196 number of mapped reads = 24,682,201 (85.16%) number of supplementary alignments = 10,208 (0.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,874,016 number of mapped paired reads (second in pair) = 11,808,185 number of mapped paired reads (both in pair) = 23,561,138 number of mapped paired reads (singletons) = 1,121,063 number of mapped bases = 1,245,668,370 bp number of sequenced bases = 1,245,532,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,609,885 duplication rate = 47.47% >>>>>>> Insert size mean insert size = 15,209.2395 std insert size = 1,152,200.2924 median insert size = 45 >>>>>>> Mapping quality mean mapping quality = 49.6189 >>>>>>> ACTG content number of A's = 306,919,190 bp (24.64%) number of C's = 330,862,064 bp (26.56%) number of T's = 312,835,917 bp (25.12%) number of G's = 294,599,564 bp (23.65%) number of N's = 315,684 bp (0.03%) GC percentage = 50.22% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 5,417,398 number of insertions = 76,419 mapped reads with insertion percentage = 0.31% number of deletions = 80,074 mapped reads with deletion percentage = 0.32% homopolymer indels = 32.91% >>>>>>> Coverage mean coverageData = 0.4024X std coverageData = 5.8001X There is a 6.46% of reference with a coverageData >= 1X There is a 4.42% of reference with a coverageData >= 2X There is a 2.13% of reference with a coverageData >= 3X There is a 1.92% of reference with a coverageData >= 4X There is a 1.26% of reference with a coverageData >= 5X There is a 1.17% of reference with a coverageData >= 6X There is a 0.89% of reference with a coverageData >= 7X There is a 0.84% of reference with a coverageData >= 8X There is a 0.7% of reference with a coverageData >= 9X There is a 0.66% of reference with a coverageData >= 10X There is a 0.58% of reference with a coverageData >= 11X There is a 0.55% of reference with a coverageData >= 12X There is a 0.49% of reference with a coverageData >= 13X There is a 0.47% of reference with a coverageData >= 14X There is a 0.43% of reference with a coverageData >= 15X There is a 0.41% of reference with a coverageData >= 16X There is a 0.38% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.33% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 110869268 0.44481039828582813 6.785076393935931 chr2 243199373 96397361 0.3963717496919698 5.525948356224605 chr3 198022430 75554966 0.3815475145921601 5.072372603254698 chr4 191154276 62798344 0.32852178519930153 4.4307258402222605 chr5 180915260 67896954 0.3752969981636707 5.008657939873138 chr6 171115067 70923031 0.41447566391099855 5.255886534627268 chr7 159138663 63462746 0.3987889856784834 5.140496148363417 chr8 146364022 55120565 0.37659914128350475 5.225016103837996 chr9 141213431 53519629 0.3789981492624452 5.1925693560755635 chr10 135534747 56256224 0.41506864656633036 5.329548754316108 chr11 135006516 58151842 0.4307335951103279 5.640891727287144 chr12 133851895 57382877 0.4287042555505098 5.694864324253075 chr13 115169878 32030661 0.278116653036656 4.1341538782994505 chr14 107349540 39375969 0.36680146929367374 5.13547477168716 chr15 102531392 39617868 0.3863974459646466 5.227657165923718 chr16 90354753 46799721 0.5179552756898135 6.650776957982575 chr17 81195210 53564380 0.6596987679445623 7.505368712335443 chr18 78077248 27926614 0.3576792819337075 4.851244984244736 chr19 59128983 49178826 0.8317211544125492 8.914975642882776 chr20 63025520 30160533 0.47854477043584887 6.78524195089219 chr21 48129895 18379718 0.3818773757973085 9.88660359460788 chr22 51304566 24081389 0.4693810098695699 6.547196927449288 chrMT 16571 9194078 554.8294007603645 362.92439862624855 chrX 155270560 43898654 0.2827236148307831 3.9488198791849913 chrY 59373566 3126152 0.05265225268766912 2.561161694963154