BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231731.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 = 2,850,674 number of mapped reads = 1,994,267 (69.96%) number of supplementary alignments = 16,892 (0.59%) number of secondary alignments = 0 number of mapped bases = 138,011,857 bp number of sequenced bases = 137,978,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 874,662 duplication rate = 12.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0181 >>>>>>> ACTG content number of A's = 24,938,196 bp (18.07%) number of C's = 18,143,029 bp (13.15%) number of T's = 26,633,382 bp (19.3%) number of G's = 68,237,440 bp (49.46%) number of N's = 26,510 bp (0.02%) GC percentage = 62.6% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 714,450 number of insertions = 7,738 mapped reads with insertion percentage = 0.38% number of deletions = 20,450 mapped reads with deletion percentage = 1.02% homopolymer indels = 44.87% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 97.9544X There is a 0.96% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 8263237 0.03315232261748307 0.5894198258520652 chr2 243199373 53066284 0.2182007434698444 349.47592360078636 chr3 198022430 3182440 0.016071108712280725 0.30795627699995354 chr4 191154276 4313878 0.02256752027875118 0.3522514508307211 chr5 180915260 4542601 0.025108998544401396 0.37712345800088237 chr6 171115067 5720049 0.03342808497395498 0.48630896021143055 chr7 159138663 4024162 0.025287142194979986 0.47826770179156275 chr8 146364022 4001724 0.027340899391245205 0.4679542448999264 chr9 141213431 2315506 0.016397207996454673 0.32795945421191064 chr10 135534747 3638565 0.02684599396492768 0.4091145589805786 chr11 135006516 6402103 0.04742069634624154 0.6344850043302082 chr12 133851895 2426524 0.018128424704035754 0.349494832992046 chr13 115169878 2203360 0.019131391282710224 0.3486505971121907 chr14 107349540 4213102 0.03924657711621307 0.5666576828705797 chr15 102531392 2812323 0.02742889709329217 0.41410489715635074 chr16 90354753 1471208 0.016282574531524645 0.32893818842542616 chr17 81195210 2116270 0.026063975941437924 0.39869703615604996 chr18 78077248 1331431 0.017052739871159392 0.5446137282662745 chr19 59128983 4600463 0.07780385805045895 0.7430599124098961 chr20 63025520 974580 0.015463259961996347 0.30829197126058505 chr21 48129895 3589459 0.07457857533244151 0.7034053149660229 chr22 51304566 875102 0.017057000345739207 0.31423563039656427 chrMT 16571 54369 3.280972783778891 4.807673479875317 chrX 155270560 11457677 0.07379168980906618 0.6762117255628807 chrY 59373566 415440 0.006997053200409085 0.18277597910381113