BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472465.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 = 31,740,070 number of mapped reads = 31,392,576 (98.91%) number of supplementary alignments = 112,767 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,731,154 number of mapped paired reads (second in pair) = 15,661,422 number of mapped paired reads (both in pair) = 31,228,948 number of mapped paired reads (singletons) = 163,628 number of mapped bases = 3,057,909,975 bp number of sequenced bases = 3,057,555,919 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,310,250 duplication rate = 47.79% >>>>>>> Insert size mean insert size = 17,658.8417 std insert size = 1,369,379.2641 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 55.0934 >>>>>>> ACTG content number of A's = 809,600,469 bp (26.48%) number of C's = 722,870,135 bp (23.64%) number of T's = 806,807,722 bp (26.39%) number of G's = 717,883,166 bp (23.48%) number of N's = 394,427 bp (0.01%) GC percentage = 47.12% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 16,620,249 number of insertions = 181,456 mapped reads with insertion percentage = 0.57% number of deletions = 143,136 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.9878X std coverageData = 34.0052X There is a 8.09% of reference with a coverageData >= 1X There is a 4.04% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 1.12% of reference with a coverageData >= 4X There is a 0.71% of reference with a coverageData >= 5X There is a 0.59% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.45% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.33% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.31% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.28% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 305843976 1.2270540180519751 36.19613486053437 chr2 243199373 271730234 1.1173146980111663 39.517658248868884 chr3 198022430 299790482 1.5139218420862728 39.344711130100066 chr4 191154276 122908102 0.6429785646019239 27.994012585657323 chr5 180915260 144518238 0.7988172915872326 31.202834969826142 chr6 171115067 208687846 1.21957609963125 33.290849503622034 chr7 159138663 167337934 1.051522809387936 35.166413414366836 chr8 146364022 157947080 1.0791386970767993 36.34253812836807 chr9 141213431 140666671 0.9961281303334383 31.016696193141176 chr10 135534747 81856455 0.6039518043295569 20.06712791936393 chr11 135006516 114018332 0.844539473931762 27.23501525718166 chr12 133851895 153556927 1.147215188847345 31.13882784589386 chr13 115169878 82044294 0.7123763211766188 27.556485055949732 chr14 107349540 68169616 0.6350247611680497 27.4718350008454 chr15 102531392 59523396 0.5805382609064744 22.335031339371106 chr16 90354753 205313657 2.2723061065752677 70.07203502516695 chr17 81195210 146413194 1.803224525190587 55.4612294238277 chr18 78077248 39531971 0.506318703753493 18.987348157617106 chr19 59128983 63170110 1.0683442669731018 29.2519742335721 chr20 63025520 82466893 1.3084682680920363 47.329874689430525 chr21 48129895 22422936 0.4658837506294165 22.431042148580456 chr22 51304566 45234996 0.8816953251295411 32.39516218277636 chrMT 16571 3683 0.22225574799348258 0.5675870814720947 chrX 155270560 69312230 0.4463964707797795 13.424686080966957 chrY 59373566 5440722 0.09163542577179885 4.593562131011477