BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751192.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 7,125,124 number of mapped reads = 6,899,603 (96.83%) number of supplementary alignments = 175,341 (2.46%) number of secondary alignments = 0 number of mapped bases = 676,370,741 bp number of sequenced bases = 676,184,770 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,970 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4961 >>>>>>> ACTG content number of A's = 196,363,840 bp (29.04%) number of C's = 141,885,324 bp (20.98%) number of T's = 197,496,636 bp (29.21%) number of G's = 140,435,322 bp (20.77%) number of N's = 3,648 bp (0%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 2,174,178 number of insertions = 109,905 mapped reads with insertion percentage = 1.57% number of deletions = 84,960 mapped reads with deletion percentage = 1.21% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.2185X std coverageData = 1.326X There is a 16.22% of reference with a coverageData >= 1X There is a 3.9% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 83943465 0.33678337355075233 3.697888720745965 chr2 243199373 50667024 0.20833533974612672 0.6483292005135717 chr3 198022430 44364896 0.22403975145643854 0.5731763178546029 chr4 191154276 29069335 0.1520726379147281 0.49393382316915235 chr5 180915260 53944258 0.29817417281438835 0.6670687135739239 chr6 171115067 42668369 0.2493548332596568 1.1575588332038345 chr7 159138663 37008855 0.23255728244996002 0.7009951114577169 chr8 146364022 31491781 0.215160669744372 0.620742371045362 chr9 141213431 29347509 0.2078237798782752 0.7354336191487704 chr10 135534747 33322236 0.2458575143095962 1.2756922678010587 chr11 135006516 30267509 0.22419294932401634 0.7663653085754092 chr12 133851895 36625132 0.2736243069252027 0.6309214416799293 chr13 115169878 17406791 0.15114013579140892 0.4646609267278862 chr14 107349540 14713504 0.1370616399474092 0.458283386956425 chr15 102531392 17206114 0.1678131318065008 0.4918869814798499 chr16 90354753 18810928 0.20818968981078395 0.7334589756173266 chr17 81195210 20685083 0.2547574296562568 0.8342671851756691 chr18 78077248 13207965 0.16916535019267073 1.3375971880092599 chr19 59128983 13385979 0.22638608548366204 2.6997429781636275 chr20 63025520 12851166 0.20390416453525492 0.5515151109040709 chr21 48129895 8729075 0.18136492921914749 0.5440641557807587 chr22 51304566 8647377 0.16854985187868074 0.5061743804895383 chrMT 16571 1008413 60.854082433166376 26.12039156762746 chrX 155270560 25859863 0.1665471097676211 0.5408442418309634 chrY 59373566 1138114 0.019168698743814713 0.6369027219245361