BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236111.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 = 4,416,049 number of mapped reads = 3,968,454 (89.86%) number of supplementary alignments = 26,572 (0.6%) number of secondary alignments = 0 number of mapped bases = 265,312,275 bp number of sequenced bases = 265,178,227 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 267,812 duplication rate = 5.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1062 >>>>>>> ACTG content number of A's = 75,217,512 bp (28.36%) number of C's = 48,921,667 bp (18.45%) number of T's = 83,705,733 bp (31.57%) number of G's = 57,330,814 bp (21.62%) number of N's = 2,501 bp (0%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,905,767 number of insertions = 19,298 mapped reads with insertion percentage = 0.48% number of deletions = 76,814 mapped reads with deletion percentage = 1.91% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.0857X std coverageData = 0.7158X There is a 5.96% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 33414297 0.13405903209364523 1.198454828428159 chr2 243199373 20810087 0.08556801254582182 0.7282670977568163 chr3 198022430 19763360 0.09980364345594588 0.4217099984671227 chr4 191154276 13137533 0.06872738227420035 0.3922870993418908 chr5 180915260 12008734 0.06637767317140633 0.34521084576550154 chr6 171115067 19555710 0.11428397477119885 0.7288621141369813 chr7 159138663 12549015 0.07885585289855049 0.6959740282895445 chr8 146364022 18787659 0.12836254937022706 1.8315057724952506 chr9 141213431 7546659 0.053441510106782976 0.4791588174018638 chr10 135534747 14621374 0.10787915515126169 0.6286865131143278 chr11 135006516 8976153 0.06648681312537537 0.4601039461006293 chr12 133851895 12704061 0.09491132717994019 0.4179132156781889 chr13 115169878 14731383 0.12791003390660882 0.48956684056963795 chr14 107349540 5155290 0.0480234009386533 0.30768156583834205 chr15 102531392 11470075 0.11186890937752995 0.4625106283323685 chr16 90354753 3045694 0.03370817692346522 0.302909195511001 chr17 81195210 6977727 0.08593766799790283 0.4613445605788915 chr18 78077248 7300698 0.09350608771456699 0.788642060666286 chr19 59128983 2423204 0.040981662072557545 0.7129292497397587 chr20 63025520 4885886 0.0775223433301304 0.3822826188733516 chr21 48129895 3849244 0.07997615619148972 0.41322227355789903 chr22 51304566 1126380 0.021954771043185512 0.18823639519732294 chrMT 16571 272017 16.415243497676663 10.018641766991143 chrX 155270560 9554623 0.061535316160384816 0.36035659287318444 chrY 59373566 645412 0.010870359378447977 0.24716623800598025