BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237861.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 = 1,883,121 number of mapped reads = 1,362,545 (72.36%) number of supplementary alignments = 10,627 (0.56%) number of secondary alignments = 0 number of mapped bases = 87,613,903 bp number of sequenced bases = 87,565,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 222,740 duplication rate = 12.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9127 >>>>>>> ACTG content number of A's = 23,881,406 bp (27.27%) number of C's = 15,795,736 bp (18.04%) number of T's = 28,132,579 bp (32.13%) number of G's = 19,675,439 bp (22.47%) number of N's = 80,394 bp (0.09%) GC percentage = 40.51% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 747,645 number of insertions = 7,470 mapped reads with insertion percentage = 0.54% number of deletions = 29,695 mapped reads with deletion percentage = 2.15% homopolymer indels = 48.89% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.369X There is a 1.28% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 7412418 0.029738814572502107 0.4529172179053012 chr2 243199373 7583303 0.03118142496197965 0.4010733620911969 chr3 198022430 6189093 0.031254504855838805 0.34086392498146983 chr4 191154276 5598962 0.029290278601981155 0.34441277807718407 chr5 180915260 5184909 0.028659323707685022 0.3367445223315963 chr6 171115067 4970251 0.029046249913223597 0.3504319704197261 chr7 159138663 5153222 0.03238196113285179 0.44425734408892276 chr8 146364022 4667648 0.031890678707913615 0.41502335754786224 chr9 141213431 3464888 0.0245365329307805 0.33942980557234664 chr10 135534747 4078664 0.0300931243852914 0.395605766486182 chr11 135006516 3913403 0.02898677127554347 0.3888728289277549 chr12 133851895 4274529 0.03193476640730413 0.34779296012846433 chr13 115169878 2935000 0.025484094026738485 0.32021438217251796 chr14 107349540 2636005 0.02455534509044007 0.31784961973752773 chr15 102531392 2609708 0.025452770601222308 0.3223901506489946 chr16 90354753 2276045 0.025190097083215977 0.3132391345790092 chr17 81195210 1987854 0.024482404811810944 0.3216000781037955 chr18 78077248 2394362 0.03066657779741417 0.4992146248129016 chr19 59128983 1327909 0.022457835948235402 0.3317793761395423 chr20 63025520 1649558 0.026172858232665117 0.32331390358455164 chr21 48129895 1095351 0.022758225423097224 0.296022633343524 chr22 51304566 808249 0.015753938937910515 0.24158690653787673 chrMT 16571 141444 8.535634542272645 6.554515929857885 chrX 155270560 4988043 0.03212484710559426 0.35992821383318063 chrY 59373566 273085 0.00459943739946494 0.12596832081809017