BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231777.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 = 1,845,113 number of mapped reads = 1,693,650 (91.79%) number of supplementary alignments = 11,550 (0.63%) number of secondary alignments = 0 number of mapped bases = 112,017,834 bp number of sequenced bases = 111,974,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,828 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2365 >>>>>>> ACTG content number of A's = 32,440,516 bp (28.97%) number of C's = 21,722,351 bp (19.4%) number of T's = 31,765,916 bp (28.37%) number of G's = 26,037,895 bp (23.25%) number of N's = 8,204 bp (0.01%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 711,582 number of insertions = 8,115 mapped reads with insertion percentage = 0.47% number of deletions = 25,653 mapped reads with deletion percentage = 1.5% homopolymer indels = 44.98% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 4.9693X There is a 3.18% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 12495903 0.05013388913482386 0.8455834690414975 chr2 243199373 9612590 0.03952555420445101 17.68283249015988 chr3 198022430 11587718 0.05851719928898964 0.26118641778031154 chr4 191154276 3366820 0.01761310325069579 0.1528889412259767 chr5 180915260 5323713 0.029426555836141184 0.18512024814032615 chr6 171115067 9912131 0.05792669911411132 0.3155308484573846 chr7 159138663 6587433 0.041394296494749364 0.528167061799655 chr8 146364022 7116559 0.04862232468577558 0.4328698806126718 chr9 141213431 5447605 0.03857710248538611 0.2921103341753069 chr10 135534747 3886485 0.02867519279022965 0.2821406974786477 chr11 135006516 3794498 0.028106036007921276 0.2542640187512017 chr12 133851895 3419694 0.025548342068672243 0.17420350713093416 chr13 115169878 3344243 0.029037479747959793 0.18169257760929042 chr14 107349540 5444662 0.05071900634134063 0.2822301768042934 chr15 102531392 1034054 0.010085242966368778 0.11001169929255063 chr16 90354753 2137393 0.023655567958887565 0.2002409527156568 chr17 81195210 2190386 0.026976788409069943 0.19698740029823342 chr18 78077248 2890920 0.03702640748813278 0.5737643606023742 chr19 59128983 1543063 0.02609655911044504 0.4516364845146475 chr20 63025520 2797824 0.04439192251011971 0.23312493156629485 chr21 48129895 1592755 0.03309284177744414 0.2014974553750234 chr22 51304566 815476 0.01589480359311489 0.13421399492695332 chrMT 16571 89934 5.4271920825538595 3.8116946413793764 chrX 155270560 5338446 0.03438157239852809 0.21749480068389884 chrY 59373566 247529 0.004169010161862267 0.09232892376767825