BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013359.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 = 1,922,310 number of mapped reads = 1,717,872 (89.36%) number of supplementary alignments = 10,485 (0.55%) number of secondary alignments = 0 number of mapped bases = 117,035,242 bp number of sequenced bases = 116,989,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,993 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4975 >>>>>>> ACTG content number of A's = 33,336,347 bp (28.5%) number of C's = 21,628,217 bp (18.49%) number of T's = 37,012,683 bp (31.64%) number of G's = 24,986,598 bp (21.36%) number of N's = 25,697 bp (0.02%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 910,721 number of insertions = 8,716 mapped reads with insertion percentage = 0.5% number of deletions = 26,154 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.3927X There is a 3.29% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 8916818 0.035774506656093746 0.6533998967226458 chr2 243199373 12177220 0.050070935010181956 0.4495621666231493 chr3 198022430 9631217 0.048637000364049665 0.24368907472239465 chr4 191154276 9626256 0.05035857005887747 0.272696298396945 chr5 180915260 5642408 0.031188126418965432 0.19636821700897628 chr6 171115067 6161161 0.03600595264939469 0.24920278790456385 chr7 159138663 6222901 0.03910364007519656 0.6468601943588151 chr8 146364022 7997989 0.05464450136523305 0.6164230860837897 chr9 141213431 4989424 0.035332503180947425 0.3874502699056236 chr10 135534747 4081017 0.030110485247004593 0.381490680482643 chr11 135006516 4661050 0.03452462990749276 0.2816775116636392 chr12 133851895 5782631 0.04320171186220412 0.23764910378512843 chr13 115169878 2573121 0.02234196167161 0.16451245923100735 chr14 107349540 4243926 0.03953371388456811 0.24166631363794525 chr15 102531392 2194585 0.02140403009450998 0.16614537137512303 chr16 90354753 2760834 0.030555492747570235 0.22396007616827457 chr17 81195210 3439996 0.042366981993149595 0.245744973157128 chr18 78077248 3154267 0.04039931069291786 0.7491499317617013 chr19 59128983 1541028 0.026062142824272827 0.4854229159672378 chr20 63025520 1951597 0.03096518680052144 0.20366006360569147 chr21 48129895 1863581 0.038719822679854174 0.2388840899680054 chr22 51304566 1262096 0.02460007165833934 0.1721612349212086 chrMT 16571 30417 1.8355560919678957 1.594695251614985 chrX 155270560 5901064 0.03800504100712975 0.2439516659311012 chrY 59373566 228638 0.0038508382669823135 0.1270663356429164