BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714162.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 792,044 number of mapped reads = 691,795 (87.34%) number of supplementary alignments = 18,961 (2.39%) number of secondary alignments = 0 number of mapped bases = 90,890,526 bp number of sequenced bases = 88,828,843 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 633,674 duplication rate = 43.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4441 >>>>>>> ACTG content number of A's = 24,032,014 bp (27.05%) number of C's = 19,734,450 bp (22.22%) number of T's = 22,832,957 bp (25.7%) number of G's = 22,228,874 bp (25.02%) number of N's = 548 bp (0%) GC percentage = 47.24% >>>>>>> Mismatches and indels general error rate = 0.044 number of mismatches = 3,660,825 number of insertions = 94,244 mapped reads with insertion percentage = 13.13% number of deletions = 326,564 mapped reads with deletion percentage = 44.92% homopolymer indels = 28.85% >>>>>>> Coverage mean coverageData = 0.0294X std coverageData = 10.3938X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7803084 0.03130617676575417 8.467831141740406 chr2 243199373 11727686 0.04822251741578298 15.984914840412406 chr3 198022430 2559898 0.012927313335161072 2.5677995465146357 chr4 191154276 2698425 0.0141164773107142 3.4892089669918396 chr5 180915260 4817681 0.026629489408466704 5.690450296699018 chr6 171115067 3185735 0.01861750140331009 4.052526409565181 chr7 159138663 2717537 0.01707653532316028 2.6511935639824653 chr8 146364022 2848573 0.019462248721205545 4.1779252813442485 chr9 141213431 3668877 0.02598107682830821 6.57726759374373 chr10 135534747 4333468 0.03197311461392258 5.665894512644248 chr11 135006516 4495777 0.03330044455039489 5.07642876247254 chr12 133851895 4783732 0.035738993459898345 7.996799173986916 chr13 115169878 4034167 0.03502796972659813 14.995389519405853 chr14 107349540 7539161 0.07023002613704726 39.98677292748219 chr15 102531392 2719803 0.026526539306127826 4.67994786474315 chr16 90354753 1592859 0.017628945319567196 2.485536414370869 chr17 81195210 3155650 0.038864977379823265 6.181773803818562 chr18 78077248 2581626 0.03306502298851517 7.3516794213393135 chr19 59128983 2068920 0.03498994731568442 4.113526122081691 chr20 63025520 2116764 0.03358582364730985 4.508835990963928 chr21 48129895 592376 0.01230785980314314 1.9418400846561297 chr22 51304566 648357 0.012637413208017392 1.5953002879654616 chrMT 16571 241533 14.575644197694768 125.47492387082376 chrX 155270560 7055857 0.04544233626773807 5.161511255535369 chrY 59373566 902980 0.015208451518643836 4.644772824639518