BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230342.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 = 3,926,997 number of mapped reads = 3,366,408 (85.72%) number of supplementary alignments = 25,391 (0.65%) number of secondary alignments = 0 number of mapped bases = 224,263,193 bp number of sequenced bases = 224,165,735 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,274 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1273 >>>>>>> ACTG content number of A's = 61,897,184 bp (27.61%) number of C's = 39,273,794 bp (17.52%) number of T's = 73,696,775 bp (32.88%) number of G's = 48,866,236 bp (21.8%) number of N's = 431,746 bp (0.19%) GC percentage = 39.32% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 2,165,257 number of insertions = 20,376 mapped reads with insertion percentage = 0.6% number of deletions = 59,346 mapped reads with deletion percentage = 1.75% homopolymer indels = 48.45% >>>>>>> Coverage mean coverageData = 0.0724X std coverageData = 0.6326X There is a 6% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 16640273 0.06676120979453849 1.106529761136389 chr2 243199373 22923389 0.09425759909339898 0.6474773891656126 chr3 198022430 17418503 0.08796227275869709 0.34146034660749264 chr4 191154276 16141989 0.08444482298685278 0.36536213927377553 chr5 180915260 13032827 0.07203829571922236 0.31618866473314605 chr6 171115067 14357887 0.08390778937076301 0.47384677578240775 chr7 159138663 9473224 0.05952811102855627 0.7261009723174601 chr8 146364022 14056172 0.09603570473077051 1.3817309677374148 chr9 141213431 9485991 0.06717484967842755 0.6056413732913355 chr10 135534747 10838247 0.07996655647278406 0.497733977635346 chr11 135006516 6392756 0.0473514626508842 0.453855119647415 chr12 133851895 10506934 0.07849671459638281 0.3365510052993478 chr13 115169878 6412733 0.055680644204554944 0.26997210700509716 chr14 107349540 8165800 0.07606739628320718 0.35717282056239114 chr15 102531392 4966848 0.048442217579568216 0.2519698033985255 chr16 90354753 4682971 0.05182871785394621 0.3286384761676818 chr17 81195210 6244246 0.07690411786606624 0.3566213939007016 chr18 78077248 4528383 0.05799875272243202 1.2208555103137093 chr19 59128983 3543031 0.05992037779509923 0.638467243162986 chr20 63025520 4030468 0.0639497778042926 0.3300908661948479 chr21 48129895 3429427 0.07125357327291074 0.3419028657014108 chr22 51304566 2370510 0.046204659444931274 0.24445666016199133 chrMT 16571 122386 7.385553074648482 4.383689448960162 chrX 155270560 13940129 0.0897796014904564 0.4095553176740937 chrY 59373566 558069 0.009399283849651207 0.18218063176899027