BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163012.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 = 96,108,720 number of mapped reads = 94,222,799 (98.04%) number of supplementary alignments = 662,619 (0.69%) number of secondary alignments = 0 number of mapped bases = 9,169,017,273 bp number of sequenced bases = 9,167,888,012 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,682,795 duplication rate = 47.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8605 >>>>>>> ACTG content number of A's = 2,190,904,997 bp (23.9%) number of C's = 2,395,466,643 bp (26.13%) number of T's = 2,180,398,161 bp (23.78%) number of G's = 2,399,144,619 bp (26.17%) number of N's = 1,973,592 bp (0.02%) GC percentage = 52.3% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 40,689,381 number of insertions = 596,696 mapped reads with insertion percentage = 0.63% number of deletions = 507,368 mapped reads with deletion percentage = 0.53% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 2.9619X std coverageData = 36.3487X There is a 10.91% of reference with a coverageData >= 1X There is a 7.1% of reference with a coverageData >= 2X There is a 5.13% of reference with a coverageData >= 3X There is a 4.54% of reference with a coverageData >= 4X There is a 4.09% of reference with a coverageData >= 5X There is a 3.83% of reference with a coverageData >= 6X There is a 3.61% of reference with a coverageData >= 7X There is a 3.44% of reference with a coverageData >= 8X There is a 3.3% of reference with a coverageData >= 9X There is a 3.17% of reference with a coverageData >= 10X There is a 3.05% of reference with a coverageData >= 11X There is a 2.95% of reference with a coverageData >= 12X There is a 2.86% of reference with a coverageData >= 13X There is a 2.77% of reference with a coverageData >= 14X There is a 2.69% of reference with a coverageData >= 15X There is a 2.62% of reference with a coverageData >= 16X There is a 2.55% of reference with a coverageData >= 17X There is a 2.48% of reference with a coverageData >= 18X There is a 2.42% of reference with a coverageData >= 19X There is a 2.36% of reference with a coverageData >= 20X There is a 2.3% of reference with a coverageData >= 21X There is a 2.25% of reference with a coverageData >= 22X There is a 2.2% of reference with a coverageData >= 23X There is a 2.15% of reference with a coverageData >= 24X There is a 2.1% of reference with a coverageData >= 25X There is a 2.06% of reference with a coverageData >= 26X There is a 2.02% of reference with a coverageData >= 27X There is a 1.97% of reference with a coverageData >= 28X There is a 1.93% of reference with a coverageData >= 29X There is a 1.9% of reference with a coverageData >= 30X There is a 1.86% of reference with a coverageData >= 31X There is a 1.82% of reference with a coverageData >= 32X There is a 1.79% of reference with a coverageData >= 33X There is a 1.76% of reference with a coverageData >= 34X There is a 1.72% of reference with a coverageData >= 35X There is a 1.69% of reference with a coverageData >= 36X There is a 1.66% of reference with a coverageData >= 37X There is a 1.63% of reference with a coverageData >= 38X There is a 1.6% of reference with a coverageData >= 39X There is a 1.58% of reference with a coverageData >= 40X There is a 1.55% of reference with a coverageData >= 41X There is a 1.52% of reference with a coverageData >= 42X There is a 1.5% of reference with a coverageData >= 43X There is a 1.47% of reference with a coverageData >= 44X There is a 1.45% of reference with a coverageData >= 45X There is a 1.43% of reference with a coverageData >= 46X There is a 1.4% of reference with a coverageData >= 47X There is a 1.38% of reference with a coverageData >= 48X There is a 1.36% of reference with a coverageData >= 49X There is a 1.34% of reference with a coverageData >= 50X There is a 1.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1520748451 6.1012824959019865 58.7661190321781 chr2 243199373 402133461 1.6535135598396464 18.580524268909294 chr3 198022430 389150459 1.9651837370140341 19.465115351865343 chr4 191154276 199731392 1.0448701236481888 17.997896645787122 chr5 180915260 434999147 2.4044359055173126 42.34784913174129 chr6 171115067 566472356 3.310476195529877 35.24685494424868 chr7 159138663 594033927 3.7328070740420887 37.75329239758865 chr8 146364022 483941245 3.306422154756037 60.447462282574605 chr9 141213431 220315632 1.560160605403037 16.802356889792545 chr10 135534747 216142821 1.5947410223888934 16.925433453768164 chr11 135006516 521673328 3.864060368760275 31.480634733869117 chr12 133851895 267224600 1.9964199983870232 19.263664011982367 chr13 115169878 101738146 0.8833746094616858 13.230709008422457 chr14 107349540 274713377 2.559054999210989 24.379302465972017 chr15 102531392 248069883 2.419452990553371 23.22441181706279 chr16 90354753 431957990 4.780689179682667 37.98447314796157 chr17 81195210 302661496 3.7275782155129593 28.419464818785226 chr18 78077248 124912071 1.5998523795305901 18.36300276748759 chr19 59128983 821140304 13.887272574940111 99.64227608799317 chr20 63025520 247713964 3.9303755684998714 32.704085151031485 chr21 48129895 131024350 2.7223069985920394 53.074535421183214 chr22 51304566 133912315 2.610144192624103 24.098125946283442 chrMT 16571 3128 0.18876350250437512 0.6277217732364834 chrX 155270560 523145055 3.369248201333208 39.91268520545881 chrY 59373566 11458375 0.1929878188552798 9.640653980075353