BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695990.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 13,998,809 number of mapped reads = 12,919,925 (92.29%) number of supplementary alignments = 185,922 (1.33%) number of secondary alignments = 0 number of mapped bases = 1,919,589,539 bp number of sequenced bases = 1,906,417,294 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,893,525 duplication rate = 19.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.0663 >>>>>>> ACTG content number of A's = 546,991,612 bp (28.69%) number of C's = 402,924,410 bp (21.14%) number of T's = 543,894,884 bp (28.53%) number of G's = 412,606,388 bp (21.64%) number of N's = 0 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 19,923,449 number of insertions = 10,379,984 mapped reads with insertion percentage = 45.7% number of deletions = 11,857,453 mapped reads with deletion percentage = 52.46% homopolymer indels = 37.39% >>>>>>> Coverage mean coverageData = 0.6201X std coverageData = 1.7195X There is a 24.36% of reference with a coverageData >= 1X There is a 13.22% of reference with a coverageData >= 2X There is a 7.75% of reference with a coverageData >= 3X There is a 4.83% of reference with a coverageData >= 4X There is a 3.15% of reference with a coverageData >= 5X There is a 2.13% of reference with a coverageData >= 6X There is a 1.48% of reference with a coverageData >= 7X There is a 1.06% of reference with a coverageData >= 8X There is a 0.77% of reference with a coverageData >= 9X There is a 0.57% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 159799970 0.6411216524110486 1.866685592940587 chr2 243199373 161055474 0.6622363866045 1.7198432001158748 chr3 198022430 137491108 0.6943208807204315 1.7520296101786164 chr4 191154276 112980696 0.591044565490128 1.5538772832244898 chr5 180915260 118267995 0.6537203937357191 1.7135506166317132 chr6 171115067 109691409 0.6410388688916564 1.7826886042351697 chr7 159138663 102086041 0.6414911315423079 1.6375501463915652 chr8 146364022 102487375 0.700222456308286 1.7290510605638685 chr9 141213431 81638144 0.5781188334698844 1.6016438985299164 chr10 135534747 90261313 0.66596437443455 1.7347652921298915 chr11 135006516 102888778 0.7621023121580295 2.222777889987795 chr12 133851895 95139436 0.7107813901327285 1.8102009300647062 chr13 115169878 58270822 0.5059554026791624 1.4890117165128305 chr14 107349540 58985870 0.5494748277449535 1.5750789739556306 chr15 102531392 60325025 0.5883566371555747 1.5895524131022434 chr16 90354753 65079725 0.7202689713511806 1.820337782747002 chr17 81195210 55678349 0.6857344047758482 1.8929337174456482 chr18 78077248 47126135 0.6035834536586125 1.7698562111233271 chr19 59128983 38400080 0.6494290625631088 1.911420926109538 chr20 63025520 48353581 0.7672063792571644 1.9064469503656258 chr21 48129895 22936205 0.47654799579346685 1.5991554276185107 chr22 51304566 22507826 0.4387099970790124 1.4677346815446726 chrMT 16571 558721 33.71679439985517 21.164025507077465 chrX 155270560 56829272 0.3660015910292331 1.2767888435699601 chrY 59373566 10750189 0.18106018762625778 1.1025041839058018