BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153397.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 59,507,194 number of mapped reads = 58,983,158 (99.12%) number of supplementary alignments = 470,065 (0.79%) number of secondary alignments = 0 number of mapped bases = 5,655,551,598 bp number of sequenced bases = 5,654,496,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,616,543 duplication rate = 33.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.3711 >>>>>>> ACTG content number of A's = 1,517,716,746 bp (26.84%) number of C's = 1,303,366,342 bp (23.05%) number of T's = 1,550,103,085 bp (27.41%) number of G's = 1,280,825,306 bp (22.65%) number of N's = 2,484,621 bp (0.04%) GC percentage = 45.7% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 16,731,575 number of insertions = 611,806 mapped reads with insertion percentage = 1.03% number of deletions = 500,347 mapped reads with deletion percentage = 0.84% homopolymer indels = 49.41% >>>>>>> Coverage mean coverageData = 1.8269X std coverageData = 16.5078X There is a 26.56% of reference with a coverageData >= 1X There is a 14.57% of reference with a coverageData >= 2X There is a 7.84% of reference with a coverageData >= 3X There is a 5.52% of reference with a coverageData >= 4X There is a 4.13% of reference with a coverageData >= 5X There is a 3.45% of reference with a coverageData >= 6X There is a 3.01% of reference with a coverageData >= 7X There is a 2.72% of reference with a coverageData >= 8X There is a 2.51% of reference with a coverageData >= 9X There is a 2.34% of reference with a coverageData >= 10X There is a 2.2% of reference with a coverageData >= 11X There is a 2.09% of reference with a coverageData >= 12X There is a 1.99% of reference with a coverageData >= 13X There is a 1.9% of reference with a coverageData >= 14X There is a 1.82% of reference with a coverageData >= 15X There is a 1.75% of reference with a coverageData >= 16X There is a 1.68% of reference with a coverageData >= 17X There is a 1.62% of reference with a coverageData >= 18X There is a 1.57% of reference with a coverageData >= 19X There is a 1.51% of reference with a coverageData >= 20X There is a 1.47% of reference with a coverageData >= 21X There is a 1.42% of reference with a coverageData >= 22X There is a 1.38% of reference with a coverageData >= 23X There is a 1.34% of reference with a coverageData >= 24X There is a 1.3% of reference with a coverageData >= 25X There is a 1.26% of reference with a coverageData >= 26X There is a 1.23% of reference with a coverageData >= 27X There is a 1.19% of reference with a coverageData >= 28X There is a 1.16% of reference with a coverageData >= 29X There is a 1.13% of reference with a coverageData >= 30X There is a 1.1% of reference with a coverageData >= 31X There is a 1.07% of reference with a coverageData >= 32X There is a 1.05% of reference with a coverageData >= 33X There is a 1.02% of reference with a coverageData >= 34X There is a 1% of reference with a coverageData >= 35X There is a 0.98% of reference with a coverageData >= 36X There is a 0.95% of reference with a coverageData >= 37X There is a 0.93% of reference with a coverageData >= 38X There is a 0.91% of reference with a coverageData >= 39X There is a 0.89% of reference with a coverageData >= 40X There is a 0.87% of reference with a coverageData >= 41X There is a 0.85% of reference with a coverageData >= 42X There is a 0.84% of reference with a coverageData >= 43X There is a 0.82% of reference with a coverageData >= 44X There is a 0.8% of reference with a coverageData >= 45X There is a 0.78% of reference with a coverageData >= 46X There is a 0.77% of reference with a coverageData >= 47X There is a 0.75% of reference with a coverageData >= 48X There is a 0.74% of reference with a coverageData >= 49X There is a 0.72% of reference with a coverageData >= 50X There is a 0.71% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 703624082 2.822958190342884 28.1285624248154 chr2 243199373 437200795 1.7977052720444309 14.861705337810426 chr3 198022430 314277184 1.5870787162848168 12.809884178820653 chr4 191154276 258067113 1.3500462474613961 11.70277297794881 chr5 180915260 283449802 1.566754523637199 12.947628240367495 chr6 171115067 306115682 1.7889463935984082 15.89618536898066 chr7 159138663 299171359 1.879941387970565 16.84252648845818 chr8 146364022 211185339 1.4428773964683752 13.889751642165477 chr9 141213431 238889633 1.6916920105142124 15.052811034089492 chr10 135534747 234421650 1.7296055453587853 14.025750546217015 chr11 135006516 274069285 2.030044868352873 15.819207584568062 chr12 133851895 312715861 2.336282657783814 17.993564851378515 chr13 115169878 125152571 1.0866779853669724 10.190354133237165 chr14 107349540 180421559 1.6806924277458477 15.601789946489758 chr15 102531392 212036606 2.068016456852551 17.10459884157845 chr16 90354753 214843842 2.37778129945195 20.486420844184252 chr17 81195210 229473827 2.82619907011756 18.76196447310805 chr18 78077248 109107282 1.397427352972277 11.958488589954115 chr19 59128983 248522742 4.203061331191845 28.690753192526056 chr20 63025520 111867959 1.7749628880491586 14.289342928582359 chr21 48129895 53182631 1.1049812387913998 10.761025384891907 chr22 51304566 79374334 1.5471202699580384 12.901426198580758 chrMT 16571 24721 1.4918230643895962 4.079216863283752 chrX 155270560 214952254 1.38437224674143 13.463071690078625 chrY 59373566 3403485 0.05732323707826476 3.081370340677925