BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089523.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 9,553,878 number of mapped reads = 7,384,790 (77.3%) number of supplementary alignments = 332 (0%) number of secondary alignments = 0 number of mapped bases = 346,682,361 bp number of sequenced bases = 346,612,441 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,349,242 duplication rate = 24.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3398 >>>>>>> ACTG content number of A's = 110,027,280 bp (31.74%) number of C's = 67,412,647 bp (19.45%) number of T's = 92,259,300 bp (26.62%) number of G's = 76,851,601 bp (22.17%) number of N's = 61,613 bp (0.02%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,974,872 number of insertions = 15,365 mapped reads with insertion percentage = 0.21% number of deletions = 45,996 mapped reads with deletion percentage = 0.62% homopolymer indels = 44.27% >>>>>>> Coverage mean coverageData = 0.112X std coverageData = 0.9678X There is a 3.93% of reference with a coverageData >= 1X There is a 1.93% of reference with a coverageData >= 2X There is a 1.25% of reference with a coverageData >= 3X There is a 0.89% of reference with a coverageData >= 4X There is a 0.65% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% 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 28060771 0.11258054598788743 1.0186612099575392 chr2 243199373 30040189 0.12352083243240927 1.075351809049187 chr3 198022430 22209743 0.11215771364890331 0.9114828515680321 chr4 191154276 21975351 0.11496133625595695 0.9343872366821616 chr5 180915260 20534994 0.11350614646879428 0.9024776374929279 chr6 171115067 19849156 0.11599887928045519 0.954749895520303 chr7 159138663 33748228 0.21206806293201044 1.5012932487484454 chr8 146364022 8947214 0.0611298724764478 0.8072273002965216 chr9 141213431 13799141 0.09771833247221363 0.8692658714264093 chr10 135534747 8571655 0.06324322869027822 0.6722961910905841 chr11 135006516 14608109 0.10820299221705713 0.9778078583507765 chr12 133851895 15538235 0.11608528216952027 0.9341427043317087 chr13 115169878 14029633 0.12181686082883582 0.9791263437084748 chr14 107349540 13908288 0.12956076011131487 1.0675593084206523 chr15 102531392 9183674 0.08956938768567582 0.7914608737763946 chr16 90354753 10300534 0.11400101995741165 0.9187326135615832 chr17 81195210 8911935 0.10975936881005666 0.8826472240044311 chr18 78077248 4774032 0.061144982978908274 0.7334668225050993 chr19 59128983 6449583 0.10907650821594547 0.9132319544038469 chr20 63025520 10226493 0.1622595577156682 1.1285178208096363 chr21 48129895 6020315 0.1250847316413219 1.0119920731909646 chr22 51304566 3701130 0.0721403627115762 0.6911629855591869 chrMT 16571 70699 4.266429304206143 14.967844177552127 chrX 155270560 20278988 0.13060420468632303 1.0200417488967848 chrY 59373566 944271 0.01590389568313953 0.31957189471149017