BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163083.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 = 75,393,580 number of mapped reads = 74,498,351 (98.81%) number of supplementary alignments = 476,925 (0.63%) number of secondary alignments = 0 number of mapped bases = 7,257,397,450 bp number of sequenced bases = 7,256,523,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,889,160 duplication rate = 45.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3256 >>>>>>> ACTG content number of A's = 1,750,662,238 bp (24.13%) number of C's = 1,878,799,660 bp (25.89%) number of T's = 1,738,337,194 bp (23.96%) number of G's = 1,888,199,038 bp (26.02%) number of N's = 525,408 bp (0.01%) GC percentage = 51.91% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 25,907,230 number of insertions = 494,459 mapped reads with insertion percentage = 0.66% number of deletions = 397,418 mapped reads with deletion percentage = 0.53% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 2.3444X std coverageData = 34.3332X There is a 8.98% of reference with a coverageData >= 1X There is a 5.8% of reference with a coverageData >= 2X There is a 4.2% of reference with a coverageData >= 3X There is a 3.67% of reference with a coverageData >= 4X There is a 3.28% of reference with a coverageData >= 5X There is a 3.04% of reference with a coverageData >= 6X There is a 2.84% of reference with a coverageData >= 7X There is a 2.68% of reference with a coverageData >= 8X There is a 2.55% of reference with a coverageData >= 9X There is a 2.43% of reference with a coverageData >= 10X There is a 2.33% of reference with a coverageData >= 11X There is a 2.24% of reference with a coverageData >= 12X There is a 2.16% of reference with a coverageData >= 13X There is a 2.08% of reference with a coverageData >= 14X There is a 2.01% of reference with a coverageData >= 15X There is a 1.95% of reference with a coverageData >= 16X There is a 1.89% of reference with a coverageData >= 17X There is a 1.83% of reference with a coverageData >= 18X There is a 1.78% of reference with a coverageData >= 19X There is a 1.73% of reference with a coverageData >= 20X There is a 1.69% of reference with a coverageData >= 21X There is a 1.64% of reference with a coverageData >= 22X There is a 1.6% of reference with a coverageData >= 23X There is a 1.56% of reference with a coverageData >= 24X There is a 1.53% of reference with a coverageData >= 25X There is a 1.49% of reference with a coverageData >= 26X There is a 1.46% of reference with a coverageData >= 27X There is a 1.43% of reference with a coverageData >= 28X There is a 1.4% of reference with a coverageData >= 29X There is a 1.37% of reference with a coverageData >= 30X There is a 1.34% of reference with a coverageData >= 31X There is a 1.31% of reference with a coverageData >= 32X There is a 1.29% of reference with a coverageData >= 33X There is a 1.26% of reference with a coverageData >= 34X There is a 1.24% of reference with a coverageData >= 35X There is a 1.21% of reference with a coverageData >= 36X There is a 1.19% of reference with a coverageData >= 37X There is a 1.17% of reference with a coverageData >= 38X There is a 1.15% of reference with a coverageData >= 39X There is a 1.13% of reference with a coverageData >= 40X There is a 1.11% of reference with a coverageData >= 41X There is a 1.09% of reference with a coverageData >= 42X There is a 1.07% of reference with a coverageData >= 43X There is a 1.06% of reference with a coverageData >= 44X There is a 1.04% of reference with a coverageData >= 45X There is a 1.02% of reference with a coverageData >= 46X There is a 1.01% of reference with a coverageData >= 47X There is a 0.99% of reference with a coverageData >= 48X There is a 0.98% of reference with a coverageData >= 49X There is a 0.96% of reference with a coverageData >= 50X There is a 0.95% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1015260776 4.073252744273002 49.43557602780363 chr2 243199373 305981040 1.258148967349517 18.415420701705987 chr3 198022430 265112143 1.3387985542849867 20.898281339699793 chr4 191154276 121722416 0.6367757946466236 11.306203278049042 chr5 180915260 405460520 2.241162630504469 39.019491893624256 chr6 171115067 403711135 2.3592962447894785 32.17799929726376 chr7 159138663 427546690 2.6866298983547447 37.657902654077894 chr8 146364022 350433905 2.3942626077875886 42.72843246722059 chr9 141213431 328039296 2.323003510905418 31.69882889848607 chr10 135534747 170242715 1.2560816968950406 17.48689928258077 chr11 135006516 476063225 3.5262240601779546 41.4105561832168 chr12 133851895 210150934 1.5700258408743484 20.0871659917344 chr13 115169878 100295672 0.8708498588493773 21.357035070544523 chr14 107349540 255009686 2.375507952805387 30.61251156089358 chr15 102531392 392865212 3.8316578399715864 46.35921146347533 chr16 90354753 347028467 3.8407328389243673 38.38952275702964 chr17 81195210 184421465 2.2713342942274553 27.803177851599184 chr18 78077248 128217725 1.642190628952496 24.905617378641207 chr19 59128983 571446426 9.664404780985326 79.7041717114831 chr20 63025520 159874385 2.5366611017251426 27.970572884020296 chr21 48129895 101875545 2.1166791450511164 54.08296911037144 chr22 51304566 90988612 1.7734993021868657 21.48379727017839 chrMT 16571 11774 0.7105183754752278 1.1922333461398142 chrX 155270560 439676046 2.831676822702256 37.324133912614634 chrY 59373566 5961640 0.10040899345678513 6.018310207593758