BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549077.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,332,749 number of mapped reads = 9,959,108 (87.88%) number of secondary alignments = 0 number of mapped bases = 394,681,095 bp number of sequenced bases = 394,643,978 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 395,765 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8758 >>>>>>> ACTG content number of A's = 117,733,958 bp (29.83%) number of C's = 79,592,090 bp (20.17%) number of T's = 119,226,185 bp (30.21%) number of G's = 77,995,499 bp (19.76%) number of N's = 96,246 bp (0.02%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,642,359 number of insertions = 10,704 mapped reads with insertion percentage = 0.11% number of deletions = 30,304 mapped reads with deletion percentage = 0.3% homopolymer indels = 44.4% >>>>>>> Coverage mean coverageData = 0.1275X std coverageData = 1.2577X There is a 10.93% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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% 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 31957457 0.1282141519719624 3.3399893618433496 chr2 243199373 34532993 0.1419945807179363 0.8402029965147393 chr3 198022430 28004041 0.14141853021397627 0.4508949019265667 chr4 191154276 27634496 0.14456645479382318 0.4468391032479556 chr5 180915260 25645551 0.14175449323622563 0.4496557564706268 chr6 171115067 24220322 0.1415440640303171 0.6358347155495673 chr7 159138663 22538295 0.14162677111344085 1.3684326657345063 chr8 146364022 20967327 0.14325465174768154 0.6999578954345383 chr9 141213431 16653650 0.11793247909966864 0.8555711541398527 chr10 135534747 19058458 0.14061676744783388 1.19008087674802 chr11 135006516 18213705 0.13490982168593996 0.8934460780455357 chr12 133851895 18184253 0.1358535342364783 0.489155169819177 chr13 115169878 13493679 0.1171632655545576 0.3673598754153216 chr14 107349540 12262454 0.11422921793609922 0.5705642834987423 chr15 102531392 11062415 0.10789295633477794 0.3661849901425877 chr16 90354753 10425916 0.11538868353721247 0.6307755059639208 chr17 81195210 9168758 0.1129224002253335 0.5203891735229179 chr18 78077248 11036420 0.14135257431204543 2.0473141871707523 chr19 59128983 6461509 0.10927820287387659 2.6374645207387846 chr20 63025520 7693856 0.12207524824864595 0.4416184527868594 chr21 48129895 5093235 0.10582269086604074 0.4987228649775761 chr22 51304566 3691369 0.07195010674098676 0.3804761403528353 chrMT 16571 6424 0.3876651982378855 0.7170281925511374 chrX 155270560 13521379 0.0870826961659699 0.5707436801362987 chrY 59373566 3153133 0.05310668050492369 0.4313953403860136