BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163159.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 = 118,969,444 number of mapped reads = 117,204,910 (98.52%) number of supplementary alignments = 1,132,208 (0.95%) number of secondary alignments = 0 number of mapped bases = 11,667,495,239 bp number of sequenced bases = 11,665,818,472 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,306,718 duplication rate = 53.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1731 >>>>>>> ACTG content number of A's = 3,034,869,861 bp (26.02%) number of C's = 2,788,878,168 bp (23.91%) number of T's = 3,063,441,172 bp (26.26%) number of G's = 2,769,749,557 bp (23.74%) number of N's = 8,879,714 bp (0.08%) GC percentage = 47.65% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 67,298,581 number of insertions = 841,945 mapped reads with insertion percentage = 0.71% number of deletions = 793,425 mapped reads with deletion percentage = 0.67% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 3.7689X std coverageData = 39.8672X There is a 10.34% of reference with a coverageData >= 1X There is a 6.97% of reference with a coverageData >= 2X There is a 5.58% of reference with a coverageData >= 3X There is a 4.96% of reference with a coverageData >= 4X There is a 4.55% of reference with a coverageData >= 5X There is a 4.28% of reference with a coverageData >= 6X There is a 4.05% of reference with a coverageData >= 7X There is a 3.88% of reference with a coverageData >= 8X There is a 3.72% of reference with a coverageData >= 9X There is a 3.59% of reference with a coverageData >= 10X There is a 3.47% of reference with a coverageData >= 11X There is a 3.37% of reference with a coverageData >= 12X There is a 3.27% of reference with a coverageData >= 13X There is a 3.18% of reference with a coverageData >= 14X There is a 3.1% of reference with a coverageData >= 15X There is a 3.02% of reference with a coverageData >= 16X There is a 2.95% of reference with a coverageData >= 17X There is a 2.88% of reference with a coverageData >= 18X There is a 2.82% of reference with a coverageData >= 19X There is a 2.76% of reference with a coverageData >= 20X There is a 2.7% of reference with a coverageData >= 21X There is a 2.64% of reference with a coverageData >= 22X There is a 2.59% of reference with a coverageData >= 23X There is a 2.54% of reference with a coverageData >= 24X There is a 2.5% of reference with a coverageData >= 25X There is a 2.45% of reference with a coverageData >= 26X There is a 2.41% of reference with a coverageData >= 27X There is a 2.36% of reference with a coverageData >= 28X There is a 2.32% of reference with a coverageData >= 29X There is a 2.28% of reference with a coverageData >= 30X There is a 2.25% of reference with a coverageData >= 31X There is a 2.21% of reference with a coverageData >= 32X There is a 2.17% of reference with a coverageData >= 33X There is a 2.14% of reference with a coverageData >= 34X There is a 2.1% of reference with a coverageData >= 35X There is a 2.07% of reference with a coverageData >= 36X There is a 2.04% of reference with a coverageData >= 37X There is a 2.01% of reference with a coverageData >= 38X There is a 1.98% of reference with a coverageData >= 39X There is a 1.95% of reference with a coverageData >= 40X There is a 1.92% of reference with a coverageData >= 41X There is a 1.9% of reference with a coverageData >= 42X There is a 1.87% of reference with a coverageData >= 43X There is a 1.84% of reference with a coverageData >= 44X There is a 1.82% of reference with a coverageData >= 45X There is a 1.79% of reference with a coverageData >= 46X There is a 1.77% of reference with a coverageData >= 47X There is a 1.75% of reference with a coverageData >= 48X There is a 1.72% of reference with a coverageData >= 49X There is a 1.7% of reference with a coverageData >= 50X There is a 1.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1572699092 6.3097098241532565 55.54849803876738 chr2 243199373 955503326 3.9288889367325797 38.79126479594201 chr3 198022430 705184923 3.5611365995256192 32.80959753881757 chr4 191154276 471166142 2.4648475140571797 29.222207992015278 chr5 180915260 633496477 3.501619913101858 46.048381765621066 chr6 171115067 354524912 2.071850937591603 24.587293881696944 chr7 159138663 651974871 4.096898005232078 48.256668990495236 chr8 146364022 520297737 3.5548198928285806 50.17941711734982 chr9 141213431 390565038 2.7657782636837145 31.05368696524063 chr10 135534747 370509771 2.7336884393195495 27.06766747116299 chr11 135006516 566633355 4.197081531975835 34.81686575710042 chr12 133851895 438459396 3.275705555009139 30.650136107661833 chr13 115169878 239108997 2.0761417929087327 22.85339227682202 chr14 107349540 257687842 2.4004559497879545 24.83406967077586 chr15 102531392 537951815 5.246703516909241 49.061768031607485 chr16 90354753 403429174 4.4649468965954675 38.57064886426859 chr17 81195210 635664389 7.828840999364371 65.03511926668462 chr18 78077248 246072794 3.151658137335988 30.886282119381832 chr19 59128983 515350026 8.715692370355837 59.67554164449459 chr20 63025520 168479600 2.673196508335036 31.240376789052867 chr21 48129895 132420713 2.7513193826830498 36.01670647951169 chr22 51304566 261380343 5.094679935505155 44.38598337089981 chrMT 16571 2018 0.12177901152616016 0.5509456996927912 chrX 155270560 623943696 4.018428838023126 40.8408580233698 chrY 59373566 14988792 0.25244890967135103 22.58868797305524