BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082892.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,492,483 number of mapped reads = 3,075,899 (88.07%) number of supplementary alignments = 13,015 (0.37%) number of secondary alignments = 0 number of mapped bases = 204,692,970 bp number of sequenced bases = 204,612,553 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,391 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1734 >>>>>>> ACTG content number of A's = 56,340,235 bp (27.54%) number of C's = 35,656,916 bp (17.43%) number of T's = 67,681,805 bp (33.08%) number of G's = 44,876,944 bp (21.93%) number of N's = 56,653 bp (0.03%) GC percentage = 39.36% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,935,145 number of insertions = 18,691 mapped reads with insertion percentage = 0.6% number of deletions = 49,530 mapped reads with deletion percentage = 1.6% homopolymer indels = 49.35% >>>>>>> Coverage mean coverageData = 0.0661X std coverageData = 0.4703X There is a 5.36% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.18% 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% 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 17478933 0.07012593561401799 0.7290925125131122 chr2 243199373 19300755 0.07936186167716806 0.5720581777125282 chr3 198022430 14177473 0.07159528847312903 0.31857395791123416 chr4 191154276 14129220 0.07391527040702976 0.34630317778623604 chr5 180915260 12240417 0.06765828930074777 0.3074477183862539 chr6 171115067 11836630 0.0691735111788841 0.4568852151688108 chr7 159138663 11101727 0.0697613439167828 0.7425377346782006 chr8 146364022 10600003 0.07242218992861511 0.5159997873195572 chr9 141213431 8970327 0.06352318569470916 0.5221502426216053 chr10 135534747 9290784 0.06854909317091948 0.4280818647666151 chr11 135006516 9683694 0.07172760461428396 0.44008036008831947 chr12 133851895 8769636 0.06551745868073067 0.30994400549675893 chr13 115169878 6679455 0.05799654489518518 0.28580861243305894 chr14 107349540 5843843 0.054437522508247356 0.3057618882897427 chr15 102531392 5799683 0.05656494939618102 0.2802284195641891 chr16 90354753 5272411 0.058352337037543556 0.33867176815007133 chr17 81195210 4872976 0.06001556003118903 0.35967309417859905 chr18 78077248 5562082 0.0712381922067745 0.7812943673359671 chr19 59128983 3298797 0.05578984844031564 0.5368097826055923 chr20 63025520 3874789 0.06147968315057139 0.3053155497057638 chr21 48129895 2663276 0.05533517162254353 0.30918801522080336 chr22 51304566 1999105 0.03896544023001773 0.23118081390584244 chrMT 16571 19120 1.1538229436968197 1.4162927015600133 chrX 155270560 10781264 0.06943533919115125 0.34843007318897407 chrY 59373566 446570 0.007521360600102746 0.19152368828261354