BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006006.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 = 33,655,654 number of mapped reads = 27,123,330 (80.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,737,821 number of mapped paired reads (second in pair) = 13,385,509 number of mapped paired reads (both in pair) = 24,309,766 number of mapped paired reads (singletons) = 2,813,564 number of mapped bases = 1,049,013,104 bp number of sequenced bases = 1,048,888,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,120,843 duplication rate = 6.56% >>>>>>> Insert size mean insert size = 79,793.6785 std insert size = 2,726,920.3583 median insert size = 109 >>>>>>> Mapping quality mean mapping quality = 47.0965 >>>>>>> ACTG content number of A's = 297,038,329 bp (28.32%) number of C's = 224,598,061 bp (21.41%) number of T's = 298,695,335 bp (28.48%) number of G's = 228,233,262 bp (21.76%) number of N's = 323,627 bp (0.03%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 5,251,737 number of insertions = 29,801 mapped reads with insertion percentage = 0.11% number of deletions = 94,827 mapped reads with deletion percentage = 0.35% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 0.3389X std coverageData = 1.8684X There is a 19.14% of reference with a coverageData >= 1X There is a 7.83% of reference with a coverageData >= 2X There is a 3.33% of reference with a coverageData >= 3X There is a 1.51% of reference with a coverageData >= 4X There is a 0.73% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% 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% 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 86809836 0.3482833288507634 2.608972470523809 chr2 243199373 88111308 0.3623007202407549 1.3268369117002734 chr3 198022430 72948203 0.36838353614790004 0.9343049170714904 chr4 191154276 68583014 0.3587835722806431 1.1001041851738966 chr5 180915260 63899474 0.3532011285283508 0.9204820855705279 chr6 171115067 59759598 0.34923632996035353 1.267830895874596 chr7 159138663 57047774 0.3584784044591351 1.9665194349586936 chr8 146364022 54354722 0.37136668736802 5.030090191695442 chr9 141213431 43575385 0.30857819041306345 1.0894134626322265 chr10 135534747 46487667 0.34299445735490985 1.6486511655736296 chr11 135006516 50827425 0.37648127294833683 1.1702080778370727 chr12 133851895 48064519 0.35908732558474427 0.9421240372649548 chr13 115169878 33423796 0.2902130017017123 0.8231048948904787 chr14 107349540 32345068 0.30130606987230685 0.92876139980084 chr15 102531392 29014945 0.28298596589813196 0.8187963807220149 chr16 90354753 31696892 0.35080492113126577 1.228308280721126 chr17 81195210 27880738 0.3433790983482893 0.9851913676517977 chr18 78077248 27838150 0.35654625019570363 1.8091182309853533 chr19 59128983 20522323 0.3470772193054631 5.1980272022575935 chr20 63025520 20818690 0.3303215903652996 0.9657662726770463 chr21 48129895 13753251 0.2857527738217588 0.9909346950448872 chr22 51304566 11635063 0.22678416186192862 0.7703351371095872 chrMT 16571 322423 19.45706354474685 11.821736936017496 chrX 155270560 56661316 0.36491989209029707 1.0711028087894068 chrY 59373566 2631524 0.04432147464412025 0.944274477445555