BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231860.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 = 1,994,059 number of mapped reads = 1,432,889 (71.86%) number of supplementary alignments = 7,186 (0.36%) number of secondary alignments = 0 number of mapped bases = 93,173,947 bp number of sequenced bases = 93,132,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,742 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.6797 >>>>>>> ACTG content number of A's = 23,645,524 bp (25.39%) number of C's = 18,714,077 bp (20.09%) number of T's = 27,828,500 bp (29.88%) number of G's = 22,939,389 bp (24.63%) number of N's = 4,569 bp (0%) GC percentage = 44.73% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 654,223 number of insertions = 5,955 mapped reads with insertion percentage = 0.41% number of deletions = 24,107 mapped reads with deletion percentage = 1.66% homopolymer indels = 44.08% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.2493X There is a 2.52% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12148032 0.048738221599054714 0.4417569838596411 chr2 243199373 10098465 0.041523400638043585 0.3410426067735122 chr3 198022430 20320462 0.10261697121886647 0.3787854954367831 chr4 191154276 2351320 0.012300640347694864 0.1301341264563791 chr5 180915260 1820872 0.010064778394039287 0.11416935242303397 chr6 171115067 4429848 0.025888123574763874 0.20889111633081592 chr7 159138663 1817757 0.011422472488662292 0.12684043468223602 chr8 146364022 2340948 0.01599401251763907 0.15390108866538965 chr9 141213431 3781396 0.026777877806821365 0.19325664494517417 chr10 135534747 4052019 0.029896532731934787 0.3144263790496943 chr11 135006516 3168423 0.02346866724566094 0.18424300299107324 chr12 133851895 3447169 0.025753606252642145 0.1885503554086422 chr13 115169878 1296236 0.011254991517834203 0.12478863313520495 chr14 107349540 2174892 0.02025990982355397 0.16714032816650906 chr15 102531392 1104061 0.01076802897594524 0.12189447832969826 chr16 90354753 3035922 0.03360002544636473 0.2157461893911561 chr17 81195210 5238520 0.06451759900614827 0.30767132368715605 chr18 78077248 784312 0.010045333565035489 0.1461662490439665 chr19 59128983 5194673 0.08785324449094617 0.44143805850824697 chr20 63025520 1506163 0.023897668753863514 0.18007115164191279 chr21 48129895 806728 0.016761474339389272 0.15335311274263239 chr22 51304566 896592 0.017475871445828038 0.15335937882374426 chrMT 16571 53934 3.2547221048820227 2.5886786841553175 chrX 155270560 1163373 0.0074925536431375015 0.10422764499987824 chrY 59373566 141830 0.002388773482125025 0.0659889518851313