BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975243.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,721,364 number of mapped reads = 2,696,017 (99.07%) number of supplementary alignments = 25,079 (0.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,347,895 number of mapped paired reads (second in pair) = 1,348,122 number of mapped paired reads (both in pair) = 2,689,770 number of mapped paired reads (singletons) = 6,247 number of mapped bases = 262,382,370 bp number of sequenced bases = 262,304,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,188 duplication rate = 1.25% >>>>>>> Insert size mean insert size = 123,525.1167 std insert size = 3,385,550.3266 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 53.5682 >>>>>>> ACTG content number of A's = 77,727,095 bp (29.63%) number of C's = 53,456,707 bp (20.38%) number of T's = 77,898,543 bp (29.7%) number of G's = 53,218,093 bp (20.29%) number of N's = 3,755 bp (0%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,249,865 number of insertions = 33,310 mapped reads with insertion percentage = 1.21% number of deletions = 33,124 mapped reads with deletion percentage = 1.19% homopolymer indels = 38.24% >>>>>>> Coverage mean coverageData = 0.0848X std coverageData = 0.9003X There is a 6.8% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 21260890 0.08529924585423601 2.2407950790136377 chr2 243199373 23109476 0.09502276142792523 0.5709824932503028 chr3 198022430 18369436 0.09276442067699099 0.35871954852494725 chr4 191154276 19150845 0.1001852817563966 0.6316891949993649 chr5 180915260 16792460 0.09281947802523678 0.34893199067293107 chr6 171115067 15872273 0.09275789255892937 0.4009858086851022 chr7 159138663 14536364 0.09134401235983741 0.6665256554914679 chr8 146364022 13793647 0.09424206038831046 1.0834112978417516 chr9 141213431 11083339 0.0784864366053113 0.9376726489771147 chr10 135534747 13151515 0.09703426826775277 1.5502387410752934 chr11 135006516 11954427 0.0885470372407803 0.4408434456398919 chr12 133851895 11781746 0.08802076354615675 0.3386065620247335 chr13 115169878 9120323 0.07919017679258113 0.3205975163733767 chr14 107349540 8024099 0.07474739994228201 0.3206340791880974 chr15 102531392 7241117 0.07062341453435061 0.302181986963591 chr16 90354753 7389479 0.08178295833535176 0.5997943216074232 chr17 81195210 6323238 0.07787698313730576 0.5772778709708255 chr18 78077248 7462266 0.09557542294523495 0.9641090370409775 chr19 59128983 4200200 0.07103453817225303 0.9792718939499485 chr20 63025520 5073686 0.08050208867772927 0.3540555462926691 chr21 48129895 3721477 0.07732152750385182 0.4359350132445444 chr22 51304566 2620328 0.05107397263627569 0.36533333758787384 chrMT 16571 131302 7.923601472451874 3.6237301583044217 chrX 155270560 7511564 0.04837725838046826 0.2893966420680944 chrY 59373566 2706873 0.04559054108355223 0.7510232264163617