BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006141.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 12,289,032 number of mapped reads = 10,702,607 (87.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,455,515 number of mapped paired reads (second in pair) = 5,247,092 number of mapped paired reads (both in pair) = 9,678,720 number of mapped paired reads (singletons) = 1,023,887 number of mapped bases = 413,407,467 bp number of sequenced bases = 413,361,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 763,761 duplication rate = 6.41% >>>>>>> Insert size mean insert size = 65,824.8722 std insert size = 2,493,504.0762 median insert size = 116 >>>>>>> Mapping quality mean mapping quality = 47.2022 >>>>>>> ACTG content number of A's = 111,840,908 bp (27.06%) number of C's = 90,146,902 bp (21.81%) number of T's = 115,617,562 bp (27.97%) number of G's = 95,737,875 bp (23.16%) number of N's = 18,243 bp (0%) GC percentage = 44.97% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 1,887,077 number of insertions = 13,387 mapped reads with insertion percentage = 0.13% number of deletions = 36,235 mapped reads with deletion percentage = 0.34% homopolymer indels = 46.13% >>>>>>> Coverage mean coverageData = 0.1335X std coverageData = 0.6829X There is a 7.52% of reference with a coverageData >= 1X There is a 3.17% of reference with a coverageData >= 2X There is a 1.37% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% 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% 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 35005056 0.14044119874028319 0.7264582694914223 chr2 243199373 35625668 0.14648749937361064 0.7503842548045182 chr3 198022430 28685826 0.14486149877061907 0.6004301208292014 chr4 191154276 25307817 0.13239472079609665 0.5984222127151866 chr5 180915260 25027731 0.13833952426124804 0.5854182441914262 chr6 171115067 24050437 0.14055125256737327 0.6623443058704578 chr7 159138663 22891045 0.14384339147049388 0.9215300418013561 chr8 146364022 20944318 0.14309744781405365 0.7211023838947485 chr9 141213431 17652384 0.1250049933281488 0.6239927835185084 chr10 135534747 20046476 0.14790654384738697 0.6369633079554109 chr11 135006516 19524962 0.14462236770853343 1.0600587241637724 chr12 133851895 18954233 0.14160601162949543 0.596939378415395 chr13 115169878 12944555 0.11239531746313042 0.5325958302040978 chr14 107349540 12872950 0.11991621016727226 0.565419406237676 chr15 102531392 12650638 0.1233830708160092 0.5644445071394306 chr16 90354753 12890628 0.1426668500770513 0.6663010111110387 chr17 81195210 12266160 0.15106999538519575 0.687871189160811 chr18 78077248 10937286 0.14008288304423844 0.8473841781063354 chr19 59128983 9056631 0.15316737309687872 0.8016714402065998 chr20 63025520 9483208 0.15046616037440072 0.6265656965589707 chr21 48129895 5563430 0.1155919829037649 0.6052287720695696 chr22 51304566 5812729 0.11329847327818736 0.5873982007588548 chrMT 16571 55421 3.3444571842375233 4.105935780689077 chrX 155270560 12618055 0.08126495454128586 0.4823497634021707 chrY 59373566 2539823 0.04277699944786877 0.35540733021240484