BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472722.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 = 13,967,574 number of mapped reads = 13,742,769 (98.39%) number of supplementary alignments = 52,112 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,917,508 number of mapped paired reads (second in pair) = 6,825,261 number of mapped paired reads (both in pair) = 13,615,244 number of mapped paired reads (singletons) = 127,525 number of mapped bases = 1,352,185,917 bp number of sequenced bases = 1,351,991,937 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,247,628 duplication rate = 46.05% >>>>>>> Insert size mean insert size = 26,807.5193 std insert size = 1,625,597.5007 median insert size = 246 >>>>>>> Mapping quality mean mapping quality = 55.256 >>>>>>> ACTG content number of A's = 374,767,594 bp (27.72%) number of C's = 303,165,798 bp (22.42%) number of T's = 371,626,698 bp (27.49%) number of G's = 302,171,829 bp (22.35%) number of N's = 260,018 bp (0.02%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 8,700,699 number of insertions = 81,278 mapped reads with insertion percentage = 0.59% number of deletions = 75,043 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.4368X std coverageData = 14.5223X There is a 4.08% of reference with a coverageData >= 1X There is a 1.77% 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 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 163355340 0.6553858896905216 20.44606163185393 chr2 243199373 88854866 0.36535812121522204 12.172024102369326 chr3 198022430 170120847 0.8590988758192696 20.491756568316266 chr4 191154276 45662333 0.2388768588153372 9.660516250493592 chr5 180915260 61785545 0.3415164923069508 11.168333976112422 chr6 171115067 88882471 0.519431003699984 13.52950647921677 chr7 159138663 74758814 0.4697715350291714 19.044459051624518 chr8 146364022 62800691 0.4290719135881631 14.48315743812108 chr9 141213431 75495920 0.5346228008580856 13.025581986779478 chr10 135534747 32872349 0.24253816624603283 8.664878384719694 chr11 135006516 65821452 0.48754277904630916 21.013028913577646 chr12 133851895 61768901 0.4614719948492324 12.578346775919721 chr13 115169878 25608515 0.2223542773918715 8.057921685184903 chr14 107349540 35784700 0.33334749268604225 11.123459064257641 chr15 102531392 33196691 0.323770996886495 11.132472698926673 chr16 90354753 53314354 0.5900558878180985 15.970514022360023 chr17 81195210 44387762 0.5466795639792051 11.955272521892296 chr18 78077248 36240383 0.4641606092468833 18.075176144989307 chr19 59128983 28195138 0.47684124721035703 17.99978345327049 chr20 63025520 31064425 0.49288645297968187 16.553836780889988 chr21 48129895 4553830 0.09461541522166213 3.17602873565714 chr22 51304566 9641729 0.1879312067467835 5.678103272910671 chrMT 16571 3627 0.2188763502504375 0.7051015096693768 chrX 155270560 55545670 0.35773471803025636 11.903800293142703 chrY 59373566 2469564 0.04159366139470215 1.4804156221739866