BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506120.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,613,885 number of mapped reads = 6,304,046 (73.18%) number of supplementary alignments = 88,563 (1.03%) number of secondary alignments = 0 number of mapped bases = 481,002,860 bp number of sequenced bases = 480,803,959 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,143,500 duplication rate = 12.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7007 >>>>>>> ACTG content number of A's = 127,531,593 bp (26.52%) number of C's = 92,200,153 bp (19.18%) number of T's = 138,296,655 bp (28.76%) number of G's = 122,697,091 bp (25.52%) number of N's = 78,467 bp (0.02%) GC percentage = 44.7% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 4,080,119 number of insertions = 41,015 mapped reads with insertion percentage = 0.63% number of deletions = 94,869 mapped reads with deletion percentage = 1.47% homopolymer indels = 40.45% >>>>>>> Coverage mean coverageData = 0.1554X std coverageData = 1.1089X There is a 8.66% of reference with a coverageData >= 1X There is a 3.3% of reference with a coverageData >= 2X There is a 1.47% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 36034640 0.14457191663325886 1.770712276861104 chr2 243199373 39202640 0.1611954813715741 1.2916501702264043 chr3 198022430 27348698 0.13810909198518573 0.6141241780429482 chr4 191154276 29165718 0.15257685368231053 1.2177926350985473 chr5 180915260 36734520 0.20304821163234102 0.8122063573087277 chr6 171115067 16677646 0.09746450907213215 0.5590447237260717 chr7 159138663 23951938 0.1505098606992821 1.0550631037148361 chr8 146364022 27309210 0.18658417298753924 1.1335341844743596 chr9 141213431 13951268 0.09879561668606437 0.9525982135993905 chr10 135534747 29845306 0.22020409275563851 1.568918571214351 chr11 135006516 20908470 0.15487008049300377 1.1125397942569497 chr12 133851895 20654793 0.15431080000772496 0.7216393567215944 chr13 115169878 8664026 0.07522822938129708 0.44895694331650043 chr14 107349540 14341888 0.13359990177880596 0.6746722575135115 chr15 102531392 17304398 0.16877170652281792 0.7100447985865103 chr16 90354753 18606186 0.20592371051028163 1.0399758720192054 chr17 81195210 13500383 0.1662706827163819 0.8595092501712137 chr18 78077248 8772045 0.11235084771430469 1.7262147161441637 chr19 59128983 13039128 0.22052007896026218 1.3909230836893556 chr20 63025520 14133018 0.22424278292348876 0.9429902921380643 chr21 48129895 8757540 0.18195634958272816 1.1300845913842674 chr22 51304566 6228729 0.12140691337297348 0.6877261005659229 chrMT 16571 117070 7.064751674612275 6.266363550235197 chrX 155270560 33543937 0.21603539653621395 0.873882315258821 chrY 59373566 2209665 0.0372163093589494 1.4718744348936985