BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975272.sorted.bam outfile = /mainsd/zhouyj/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 = 5,790,386 number of mapped reads = 5,732,341 (99%) number of supplementary alignments = 27,837 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,864,954 number of mapped paired reads (second in pair) = 2,867,387 number of mapped paired reads (both in pair) = 5,713,622 number of mapped paired reads (singletons) = 18,719 number of mapped bases = 534,017,536 bp number of sequenced bases = 533,709,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,642 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 64,370.8153 std insert size = 2,447,267.7116 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 52.93 >>>>>>> ACTG content number of A's = 157,682,212 bp (29.54%) number of C's = 105,992,625 bp (19.86%) number of T's = 156,510,434 bp (29.33%) number of G's = 113,509,953 bp (21.27%) number of N's = 14,570 bp (0%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 4,494,229 number of insertions = 88,718 mapped reads with insertion percentage = 1.52% number of deletions = 184,439 mapped reads with deletion percentage = 3.15% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 0.1725X std coverageData = 1.7958X There is a 11.06% of reference with a coverageData >= 1X There is a 3.65% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 0.01% 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% 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 48840582 0.1959496903319651 1.913211703975558 chr2 243199373 51816685 0.21306257644011278 1.793640301446006 chr3 198022430 36707055 0.1853681676363632 0.6367559198628734 chr4 191154276 23660609 0.12377755546519922 1.1670666946290305 chr5 180915260 32465781 0.17945297151826772 0.5658985876381569 chr6 171115067 42327303 0.2473616364828937 1.4371981860275593 chr7 159138663 30484292 0.19155805022692693 1.9512829982577684 chr8 146364022 27445826 0.1875175717704724 0.7822243878649164 chr9 141213431 22710602 0.16082465980165866 2.6153350915588227 chr10 135534747 29120920 0.21485944117341363 4.93358754635978 chr11 135006516 19567732 0.1449391672324912 1.7953655110088285 chr12 133851895 22959220 0.1715270448729919 0.5616433794584789 chr13 115169878 17769994 0.15429376420803362 0.528073214353437 chr14 107349540 15829128 0.14745408317539135 0.5810090541234981 chr15 102531392 15470754 0.1508879738997399 0.5222874649838781 chr16 90354753 17729301 0.19621879769844536 2.7859375815977394 chr17 81195210 10682143 0.13156124603902128 1.3862079597122854 chr18 78077248 14905203 0.1909032833739222 2.595574143380131 chr19 59128983 6858269 0.11598827938576248 1.2530994900999721 chr20 63025520 11094529 0.17603232785703316 0.63032827147831 chr21 48129895 6567478 0.13645319608530207 0.7508921820687839 chr22 51304566 5157424 0.10052563352743302 0.43239029413804797 chrMT 16571 128971 7.782934041397622 8.071121541829342 chrX 155270560 16566539 0.10669465608934495 0.803453010906835 chrY 59373566 7151196 0.1204441047047772 2.456706373539967