BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504602.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 = 399,979,832 number of mapped reads = 344,313,098 (86.08%) number of supplementary alignments = 1,893,890 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 172,493,575 number of mapped paired reads (second in pair) = 171,819,523 number of mapped paired reads (both in pair) = 342,249,944 number of mapped paired reads (singletons) = 2,063,154 number of mapped bases = 34,179,062,839 bp number of sequenced bases = 34,170,211,435 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,804,887 duplication rate = 20.98% >>>>>>> Insert size mean insert size = 29,608.9272 std insert size = 1,669,709.4878 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.9649 >>>>>>> ACTG content number of A's = 9,016,738,739 bp (26.39%) number of C's = 7,993,995,010 bp (23.39%) number of T's = 9,044,550,708 bp (26.47%) number of G's = 8,105,977,235 bp (23.72%) number of N's = 8,949,743 bp (0.03%) GC percentage = 47.12% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 179,791,828 number of insertions = 2,568,327 mapped reads with insertion percentage = 0.73% number of deletions = 3,449,965 mapped reads with deletion percentage = 0.97% homopolymer indels = 40.48% >>>>>>> Coverage mean coverageData = 11.0408X std coverageData = 22.8236X There is a 77.9% of reference with a coverageData >= 1X There is a 68.95% of reference with a coverageData >= 2X There is a 61.45% of reference with a coverageData >= 3X There is a 55.22% of reference with a coverageData >= 4X There is a 49.88% of reference with a coverageData >= 5X There is a 45.28% of reference with a coverageData >= 6X There is a 41.27% of reference with a coverageData >= 7X There is a 37.76% of reference with a coverageData >= 8X There is a 34.66% of reference with a coverageData >= 9X There is a 31.92% of reference with a coverageData >= 10X There is a 29.47% of reference with a coverageData >= 11X There is a 27.27% of reference with a coverageData >= 12X There is a 25.3% of reference with a coverageData >= 13X There is a 23.52% of reference with a coverageData >= 14X There is a 21.91% of reference with a coverageData >= 15X There is a 20.44% of reference with a coverageData >= 16X There is a 19.11% of reference with a coverageData >= 17X There is a 17.9% of reference with a coverageData >= 18X There is a 16.79% of reference with a coverageData >= 19X There is a 15.77% of reference with a coverageData >= 20X There is a 14.83% of reference with a coverageData >= 21X There is a 13.97% of reference with a coverageData >= 22X There is a 13.18% of reference with a coverageData >= 23X There is a 12.44% of reference with a coverageData >= 24X There is a 11.76% of reference with a coverageData >= 25X There is a 11.13% of reference with a coverageData >= 26X There is a 10.55% of reference with a coverageData >= 27X There is a 10% of reference with a coverageData >= 28X There is a 9.5% of reference with a coverageData >= 29X There is a 9.02% of reference with a coverageData >= 30X There is a 8.58% of reference with a coverageData >= 31X There is a 8.17% of reference with a coverageData >= 32X There is a 7.78% of reference with a coverageData >= 33X There is a 7.42% of reference with a coverageData >= 34X There is a 7.08% of reference with a coverageData >= 35X There is a 6.76% of reference with a coverageData >= 36X There is a 6.46% of reference with a coverageData >= 37X There is a 6.18% of reference with a coverageData >= 38X There is a 5.91% of reference with a coverageData >= 39X There is a 5.66% of reference with a coverageData >= 40X There is a 5.42% of reference with a coverageData >= 41X There is a 5.2% of reference with a coverageData >= 42X There is a 4.99% of reference with a coverageData >= 43X There is a 4.79% of reference with a coverageData >= 44X There is a 4.6% of reference with a coverageData >= 45X There is a 4.42% of reference with a coverageData >= 46X There is a 4.25% of reference with a coverageData >= 47X There is a 4.09% of reference with a coverageData >= 48X There is a 3.93% of reference with a coverageData >= 49X There is a 3.79% of reference with a coverageData >= 50X There is a 3.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3507490200 14.072142271613437 23.73690892079408 chr2 243199373 2344744009 9.641241998596765 17.202012648355407 chr3 198022430 2532109522 12.786983383650023 21.128270794241622 chr4 191154276 1433796053 7.500727072409304 11.893969299306008 chr5 180915260 1391441659 7.691123783587963 12.92618969247052 chr6 171115067 1747876360 10.214625693948973 16.644048812737378 chr7 159138663 2782116908 17.482344362790077 25.95033734628935 chr8 146364022 2611218178 17.840574085891134 43.831794064424 chr9 141213431 1344086648 9.518121884596091 18.560832677861058 chr10 135534747 1609908340 11.87819637129658 22.4340266734181 chr11 135006516 1741685322 12.900750079351726 21.84625573234595 chr12 133851895 1165170516 8.704923572430559 14.647493743549283 chr13 115169878 777535386 6.75120439043966 12.673582174522759 chr14 107349540 1140705579 10.626087256638455 18.459449131462904 chr15 102531392 761386534 7.4258870297986395 13.862030532946374 chr16 90354753 996194868 11.025373153308271 18.958803758336753 chr17 81195210 1237480403 15.240805498255378 46.79723540051106 chr18 78077248 447650525 5.733431139888537 26.78043828407883 chr19 59128983 1004118481 16.981832428946056 29.43887270819065 chr20 63025520 1535514065 24.36337002852178 36.31050871423118 chr21 48129895 324013720 6.732067875901246 17.018945712299203 chr22 51304566 701516839 13.673575155084636 25.502006032737746 chrMT 16571 237835 14.352483253877255 11.529926126149162 chrX 155270560 1006513001 6.482317066416196 11.43088975151788 chrY 59373566 34551888 0.5819405895209326 13.922241424639743