BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971310.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,262,207 number of mapped reads = 9,526,887 (92.83%) number of supplementary alignments = 1,431 (0.01%) number of secondary alignments = 0 number of mapped bases = 458,055,725 bp number of sequenced bases = 457,957,479 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 826,664 duplication rate = 6.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.2093 >>>>>>> ACTG content number of A's = 130,370,457 bp (28.47%) number of C's = 96,412,236 bp (21.05%) number of T's = 131,027,028 bp (28.61%) number of G's = 100,125,575 bp (21.86%) number of N's = 22,183 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 2,341,657 number of insertions = 29,972 mapped reads with insertion percentage = 0.31% number of deletions = 67,629 mapped reads with deletion percentage = 0.71% homopolymer indels = 41.03% >>>>>>> Coverage mean coverageData = 0.148X std coverageData = 1.2633X There is a 10.21% of reference with a coverageData >= 1X There is a 2.84% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.12% 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 0.01% 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 0.01% 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% 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 35566916 0.1426953957318325 2.3696661912786796 chr2 243199373 38165920 0.15693264143407146 1.1577003679113285 chr3 198022430 32016171 0.16167951782027926 0.5543920962908171 chr4 191154276 30464740 0.15937252693212053 0.7316197366393701 chr5 180915260 30204539 0.166954070098896 0.5668031568859768 chr6 171115067 28298321 0.16537597475270838 0.6095564918160293 chr7 159138663 25870358 0.16256488217448453 1.9334844425552677 chr8 146364022 23874411 0.16311666401187036 2.1364433780609495 chr9 141213431 18493531 0.1309615584653559 1.2088545372859505 chr10 135534747 23420634 0.17280169490411193 1.3654174940967707 chr11 135006516 20632645 0.1528270309560466 1.0466118020338058 chr12 133851895 19709725 0.14725024998712197 0.5699423618575117 chr13 115169878 14994773 0.13019700342132862 0.48332315131357645 chr14 107349540 14129843 0.1316246254990939 0.7334566199287794 chr15 102531392 13522618 0.13188758814471183 0.5043187402289695 chr16 90354753 12855459 0.1422776176478508 0.6655464928138249 chr17 81195210 13097443 0.1613080747004657 0.7523054904419663 chr18 78077248 14071293 0.18022270713230057 2.3302607350104476 chr19 59128983 9468652 0.16013554638678631 2.061096173792518 chr20 63025520 8547284 0.13561623926307947 0.5537573652249903 chr21 48129895 5517384 0.11463528021409562 0.7058270984218221 chr22 51304566 4575631 0.08918564870035155 0.472509676861355 chrMT 16571 69581 4.198962042121779 3.839208308016102 chrX 155270560 16685437 0.10746040331148415 0.6292727623043092 chrY 59373566 3802416 0.06404223724746463 0.6640508219500509