BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003994.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,102,995 number of mapped reads = 2,696,138 (86.89%) number of supplementary alignments = 21,513 (0.69%) number of secondary alignments = 0 number of mapped bases = 182,908,933 bp number of sequenced bases = 182,836,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,944 duplication rate = 4.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6986 >>>>>>> ACTG content number of A's = 50,541,123 bp (27.64%) number of C's = 34,308,184 bp (18.76%) number of T's = 58,368,876 bp (31.92%) number of G's = 39,593,556 bp (21.66%) number of N's = 24,891 bp (0.01%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,712,643 number of insertions = 14,831 mapped reads with insertion percentage = 0.54% number of deletions = 43,199 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.0591X std coverageData = 0.5099X There is a 4.86% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 15305531 0.06140619003713536 0.9620016313307308 chr2 243199373 13326981 0.05479858288943862 0.5223826095823424 chr3 198022430 14533100 0.0733911809889415 0.31645648826076117 chr4 191154276 10836132 0.056687887013314835 0.31647726045044233 chr5 180915260 9640602 0.05328794265337263 0.2726525911413049 chr6 171115067 11416963 0.06672096852815422 0.3553568729368222 chr7 159138663 11371858 0.07145880068126499 0.7236286429719845 chr8 146364022 8205619 0.05606308768967827 0.708737898810845 chr9 141213431 8290875 0.058711660366073816 0.46657761902138206 chr10 135534747 9302331 0.06863428903585883 0.491575152457739 chr11 135006516 9639735 0.07140199810800243 0.5152841702558065 chr12 133851895 7131074 0.05327585388312956 0.28220733859431746 chr13 115169878 7162276 0.062188795580733355 0.29105538903503286 chr14 107349540 4362115 0.04063468739595903 0.27518016370487525 chr15 102531392 4415694 0.04306675169298394 0.24286696070874364 chr16 90354753 5571739 0.061665145606673286 0.33176358213128243 chr17 81195210 3903768 0.0480787967664595 0.3046042866497913 chr18 78077248 5773338 0.07394392281859115 0.9055606902596773 chr19 59128983 2794001 0.04725264765673375 0.6362069633324687 chr20 63025520 3314350 0.05258742807675367 0.2802033369995153 chr21 48129895 2197642 0.045660643971901456 0.30896975361244366 chr22 51304566 1634393 0.03185667723999459 0.20497353870533624 chrMT 16571 107696 6.499064630981835 4.2901006085322875 chrX 155270560 12144556 0.07821544534907325 0.37562776982465207 chrY 59373566 526564 0.008868660507943889 0.20667261584257415