BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472424.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 22,163,910 number of mapped reads = 21,980,593 (99.17%) number of supplementary alignments = 84,412 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,021,199 number of mapped paired reads (second in pair) = 10,959,394 number of mapped paired reads (both in pair) = 21,872,444 number of mapped paired reads (singletons) = 108,149 number of mapped bases = 2,155,949,639 bp number of sequenced bases = 2,155,690,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,222,496 duplication rate = 48.27% >>>>>>> Insert size mean insert size = 18,463.1109 std insert size = 1,346,420.9708 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 54.8078 >>>>>>> ACTG content number of A's = 594,196,916 bp (27.56%) number of C's = 485,193,050 bp (22.51%) number of T's = 595,561,895 bp (27.63%) number of G's = 480,472,010 bp (22.29%) number of N's = 266,855 bp (0.01%) GC percentage = 44.8% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 11,751,388 number of insertions = 129,399 mapped reads with insertion percentage = 0.58% number of deletions = 109,468 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.6964X std coverageData = 20.4603X There is a 6.03% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.29% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 217397245 0.872203423717849 25.545170422252493 chr2 243199373 172122393 0.7077419274432093 19.330240008899324 chr3 198022430 161350376 0.8148085850678632 18.45992438316471 chr4 191154276 59103727 0.30919385240432706 11.180589018655075 chr5 180915260 90777295 0.5017669322090353 15.003574944911241 chr6 171115067 172947471 1.0107086069749778 22.113293717701175 chr7 159138663 124300016 0.7810799315311578 20.074553963363993 chr8 146364022 192422163 1.3146821218126952 35.62616019725796 chr9 141213431 57259553 0.40548234395636207 10.521725543456341 chr10 135534747 43715682 0.32254224815131727 11.063027933102113 chr11 135006516 61204554 0.4533451852057274 13.089817575085238 chr12 133851895 114918794 0.8585518643572435 21.42792984025353 chr13 115169878 94332299 0.8190709292928139 26.68588431549977 chr14 107349540 43920594 0.4091363037047015 11.217843634686927 chr15 102531392 35899710 0.35013383998531883 10.701353391304547 chr16 90354753 112713587 1.2474560912141501 31.720370591308715 chr17 81195210 75624241 0.9313879599547806 20.000881091622688 chr18 78077248 15490252 0.19839649061401343 13.30334632052811 chr19 59128983 43106234 0.7290203858233111 17.592940015972346 chr20 63025520 98354478 1.560550043855251 38.29695218323617 chr21 48129895 23789989 0.4942871577010505 23.69816856975496 chr22 51304566 15819008 0.3083352854013033 7.865659358183034 chrMT 16571 7014 0.4232695673163961 0.8342578714378001 chrX 155270560 128983134 0.8306992259189379 21.85358219255144 chrY 59373566 389830 0.006565716467156445 0.5439829813789072