BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004049.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,685,949 number of mapped reads = 3,121,737 (84.69%) number of supplementary alignments = 37,502 (1.02%) number of secondary alignments = 0 number of mapped bases = 203,059,900 bp number of sequenced bases = 202,943,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 338,261 duplication rate = 8.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1349 >>>>>>> ACTG content number of A's = 56,780,426 bp (27.98%) number of C's = 36,305,505 bp (17.89%) number of T's = 65,501,041 bp (32.28%) number of G's = 44,204,161 bp (21.78%) number of N's = 152,255 bp (0.08%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,811,079 number of insertions = 14,190 mapped reads with insertion percentage = 0.45% number of deletions = 68,944 mapped reads with deletion percentage = 2.18% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.0656X std coverageData = 0.5509X There is a 4% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% 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 13656697 0.054791024974016014 0.6918708427572859 chr2 243199373 30710649 0.12627766519776348 0.7114607801979066 chr3 198022430 3825264 0.019317326830096973 0.21268430146245063 chr4 191154276 14271560 0.07465990454746615 0.4341182737151885 chr5 180915260 7216706 0.03988997943014868 0.3034475505273282 chr6 171115067 3066404 0.017920128564716045 0.22005011970386062 chr7 159138663 31866501 0.20024361396073811 1.2034170427428417 chr8 146364022 4006465 0.027373291231365587 0.368994534741233 chr9 141213431 10843935 0.07679110211549212 0.5226464814767132 chr10 135534747 10424558 0.07691428383306016 0.5920223420211359 chr11 135006516 1581517 0.01171437532689163 0.17405695674793223 chr12 133851895 8136077 0.060784174927071444 0.38036554521290883 chr13 115169878 16773033 0.14563732541246593 0.5764259685382679 chr14 107349540 2319901 0.02161072138734828 0.3005814466526559 chr15 102531392 4146485 0.040441126557610764 0.34331321218891664 chr16 90354753 7914917 0.08759823625437833 0.5546686513359839 chr17 81195210 4188803 0.05158928710203471 0.3380789629023529 chr18 78077248 6163452 0.07894043601536775 1.0690951564853386 chr19 59128983 699821 0.011835498675835504 0.4843042056461352 chr20 63025520 547398 0.008685338891293559 0.22369199767398792 chr21 48129895 2366423 0.049167424944517334 0.3558189773710503 chr22 51304566 356569 0.006950044173456218 0.11050351107745461 chrMT 16571 20702 1.2492909299378432 1.5538557145778111 chrX 155270560 17446995 0.1123651193117356 0.5555371669547625 chrY 59373566 509068 0.008573983917354736 0.16968160160521137