BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472764.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,493,204 number of mapped reads = 15,346,258 (99.05%) number of supplementary alignments = 49,487 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,696,863 number of mapped paired reads (second in pair) = 7,649,395 number of mapped paired reads (both in pair) = 15,264,382 number of mapped paired reads (singletons) = 81,876 number of mapped bases = 1,513,577,269 bp number of sequenced bases = 1,513,372,545 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,573,300 duplication rate = 46.66% >>>>>>> Insert size mean insert size = 21,376.4567 std insert size = 1,419,721.9782 median insert size = 246 >>>>>>> Mapping quality mean mapping quality = 55.1613 >>>>>>> ACTG content number of A's = 410,176,805 bp (27.1%) number of C's = 348,589,222 bp (23.03%) number of T's = 407,694,707 bp (26.94%) number of G's = 346,617,716 bp (22.9%) number of N's = 294,095 bp (0.02%) GC percentage = 45.94% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 9,321,511 number of insertions = 84,495 mapped reads with insertion percentage = 0.55% number of deletions = 84,238 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.4889X std coverageData = 17.4684X There is a 4.24% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 169621477 0.6805257949588017 21.626382840099883 chr2 243199373 102240890 0.4203994802239889 15.838787115151108 chr3 198022430 161226913 0.8141851051923764 17.288808420376384 chr4 191154276 59896788 0.3133426531353136 10.236474593000551 chr5 180915260 86687153 0.47915887802941554 18.47021117031461 chr6 171115067 79336093 0.4636417727025756 13.669948817898849 chr7 159138663 68795627 0.4322998930812935 16.576326872061014 chr8 146364022 64766348 0.4425018328616304 16.907258775256473 chr9 141213431 89567280 0.6342688465660182 19.060333374635245 chr10 135534747 54676523 0.4034133254404496 26.349181783719512 chr11 135006516 48821392 0.36162248642872913 10.488838492132599 chr12 133851895 94745626 0.7078392577109199 26.351600144802855 chr13 115169878 22876026 0.19862855112167438 6.465423514178319 chr14 107349540 26827726 0.249910022902753 10.76505223097549 chr15 102531392 38560473 0.3760845556451628 10.543012674249706 chr16 90354753 71229949 0.7883364918279396 24.728248368155263 chr17 81195210 52806023 0.6503588450599488 15.16216489818334 chr18 78077248 20360230 0.26077033350355794 9.213181305956077 chr19 59128983 43369845 0.7334786224887379 23.372257367940957 chr20 63025520 30268901 0.4802642009141694 11.883138417700717 chr21 48129895 7114766 0.1478242576677136 6.70571599334878 chr22 51304566 11464869 0.22346683529103434 7.461137693263238 chrMT 16571 4014 0.24223040251040975 0.8818873927567521 chrX 155270560 106678264 0.6870475897040624 25.3516777987185 chrY 59373566 1634073 0.02752189417088406 0.8326217133508492