BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038430.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 16,570,774 number of mapped reads = 15,774,342 (95.19%) number of supplementary alignments = 275,420 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,961,404 number of mapped paired reads (second in pair) = 7,812,938 number of mapped paired reads (both in pair) = 15,601,332 number of mapped paired reads (singletons) = 173,010 number of mapped bases = 2,266,118,795 bp number of sequenced bases = 2,264,476,565 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,657,860 duplication rate = 10.97% >>>>>>> Insert size mean insert size = 78,488.0598 std insert size = 2,678,980.0781 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 53.7887 >>>>>>> ACTG content number of A's = 666,964,976 bp (29.45%) number of C's = 460,915,157 bp (20.35%) number of T's = 664,837,771 bp (29.36%) number of G's = 471,708,969 bp (20.83%) number of N's = 49,692 bp (0%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.0143 number of mismatches = 31,182,857 number of insertions = 425,210 mapped reads with insertion percentage = 2.52% number of deletions = 816,329 mapped reads with deletion percentage = 4.96% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.732X std coverageData = 11.1099X There is a 26.76% of reference with a coverageData >= 1X There is a 16.04% of reference with a coverageData >= 2X There is a 9.02% of reference with a coverageData >= 3X There is a 5.71% of reference with a coverageData >= 4X There is a 3.5% of reference with a coverageData >= 5X There is a 2.26% of reference with a coverageData >= 6X There is a 1.46% of reference with a coverageData >= 7X There is a 0.97% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 176977656 0.7100389771947649 13.632956869525348 chr2 243199373 213930894 0.8796523254194409 16.172134078652988 chr3 198022430 154664076 0.7810432181849298 1.746470052600544 chr4 191154276 156067196 0.8164462719107576 8.142108044904546 chr5 180915260 140309604 0.7755542788375066 1.8935452434444164 chr6 171115067 139689917 0.8163507717295286 13.770478181723815 chr7 159138663 121207323 0.7616459803988677 10.921452205462499 chr8 146364022 116735274 0.7975680936125136 3.7579999315373374 chr9 141213431 100443435 0.7112881139471783 24.35832135640357 chr10 135534747 119728643 0.8833796915561439 18.37938012449478 chr11 135006516 105727254 0.783127045512381 7.127231739737185 chr12 133851895 97490522 0.7283462217699644 1.7354943528884579 chr13 115169878 72091128 0.6259547136100987 1.5138086261684465 chr14 107349540 66971344 0.6238624217672475 1.783403194892182 chr15 102531392 61193357 0.5968255751370273 1.501409952207493 chr16 90354753 73555224 0.814071441266626 12.534660633362433 chr17 81195210 51296088 0.6317624894374927 8.488153586732798 chr18 78077248 68020699 0.8711974453812716 19.37156854994177 chr19 59128983 28612689 0.4839029448553174 7.473923114176691 chr20 63025520 45253663 0.7180212555168128 2.8520204586154363 chr21 48129895 30254943 0.6286102016220896 4.188301552271601 chr22 51304566 19089159 0.37207524570035344 1.3795125081231336 chrMT 16571 4159288 250.99800856918714 143.61615945385142 chrX 155270560 72087073 0.46426748895605197 2.393276755382167 chrY 59373566 30562346 0.5147466803661414 13.404060352021316