BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038391.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 = 14,020,924 number of mapped reads = 13,639,571 (97.28%) number of supplementary alignments = 141,807 (1.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,896,286 number of mapped paired reads (second in pair) = 6,743,285 number of mapped paired reads (both in pair) = 13,472,194 number of mapped paired reads (singletons) = 167,377 number of mapped bases = 2,002,538,912 bp number of sequenced bases = 2,001,832,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,364,549 duplication rate = 7.46% >>>>>>> Insert size mean insert size = 93,133.3512 std insert size = 3,014,112.6736 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 54.4103 >>>>>>> ACTG content number of A's = 580,371,365 bp (28.99%) number of C's = 424,357,430 bp (21.2%) number of T's = 574,898,930 bp (28.72%) number of G's = 422,160,828 bp (21.09%) number of N's = 44,329 bp (0%) GC percentage = 42.29% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 21,655,150 number of insertions = 241,492 mapped reads with insertion percentage = 1.67% number of deletions = 257,360 mapped reads with deletion percentage = 1.81% homopolymer indels = 44.4% >>>>>>> Coverage mean coverageData = 0.6469X std coverageData = 6.203X There is a 37.36% of reference with a coverageData >= 1X There is a 15.75% of reference with a coverageData >= 2X There is a 5.49% of reference with a coverageData >= 3X There is a 2.22% of reference with a coverageData >= 4X There is a 0.8% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% 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 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 138074107 0.5539569227392216 15.180311358131158 chr2 243199373 195869046 0.8053846668428705 5.510571604913509 chr3 198022430 128570015 0.6492699589637396 1.038163521294626 chr4 191154276 112622279 0.5891695511953915 4.389321764420499 chr5 180915260 112424121 0.6214186741350619 1.084582054418555 chr6 171115067 133599983 0.7807610711451844 6.0072737492789186 chr7 159138663 137058441 0.8612516808690293 5.057738875615556 chr8 146364022 89790719 0.6134753457376294 4.056253695628525 chr9 141213431 81781767 0.5791358967830759 7.346556294233282 chr10 135534747 80435340 0.5934665595384185 10.105074116042509 chr11 135006516 108645070 0.8047394542053067 3.9103567127362617 chr12 133851895 76703903 0.5730505571101552 0.9958800807928081 chr13 115169878 108757847 0.9443254511392293 1.2938088166073616 chr14 107349540 42762763 0.39835068692422904 0.8805054139189934 chr15 102531392 41039258 0.4002604197551517 0.8185461027897785 chr16 90354753 70671036 0.7821507298016741 4.3123389930749285 chr17 81195210 56881902 0.7005573604649831 3.1204236368758274 chr18 78077248 34329135 0.4396816726942015 7.070341672675878 chr19 59128983 39814085 0.673342969555218 7.082987500494712 chr20 63025520 72070535 1.1435135322961238 1.9237009829082248 chr21 48129895 20169653 0.4190670476218575 2.897123657450718 chr22 51304566 19481015 0.3797130844065614 2.6545140398051137 chrMT 16571 3490920 210.66441373483798 25.814912350349516 chrX 155270560 78659461 0.5065961055334637 1.3386231196329839 chrY 59373566 18836511 0.3172541632416015 5.921525116560679