BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004081.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 = 2,160,428 number of mapped reads = 1,857,458 (85.98%) number of supplementary alignments = 22,527 (1.04%) number of secondary alignments = 0 number of mapped bases = 120,239,138 bp number of sequenced bases = 120,185,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 181,099 duplication rate = 7.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1683 >>>>>>> ACTG content number of A's = 33,114,231 bp (27.55%) number of C's = 22,275,631 bp (18.53%) number of T's = 37,873,559 bp (31.51%) number of G's = 26,908,061 bp (22.39%) number of N's = 14,203 bp (0.01%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 922,371 number of insertions = 8,201 mapped reads with insertion percentage = 0.44% number of deletions = 30,679 mapped reads with deletion percentage = 1.63% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 0.0388X std coverageData = 0.378X There is a 2.5% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 3469633 0.013920258196668646 0.4588922696350678 chr2 243199373 13192178 0.054244292809093715 0.46273697239595685 chr3 198022430 3123018 0.01577103159475419 0.17570178704381348 chr4 191154276 7937422 0.041523643447034374 0.32007462350924415 chr5 180915260 13158784 0.0727345167013551 0.39840651054937365 chr6 171115067 3911389 0.022858238427361864 0.23222412916080504 chr7 159138663 9421380 0.059202332245307354 0.4448201920096896 chr8 146364022 10749276 0.07344206488121788 0.5119617332729178 chr9 141213431 7080890 0.0501431765367984 0.5023517459448827 chr10 135534747 6989338 0.05156860624087785 0.41981009199266534 chr11 135006516 7206373 0.05337796436432742 0.3662753919667044 chr12 133851895 6708526 0.05011902147519092 0.3425545649470761 chr13 115169878 3919202 0.03402974864660358 0.26477055277770334 chr14 107349540 2940818 0.027394789022850027 0.3324712426109579 chr15 102531392 3751761 0.03659133975280468 0.28787548899474724 chr16 90354753 628998 0.006961426810607296 0.2264356380522912 chr17 81195210 1088811 0.013409793508755012 0.16952536981968178 chr18 78077248 637529 0.008165362078335547 0.6568804237795257 chr19 59128983 1736751 0.029372245418122615 0.38571298664846193 chr20 63025520 1254000 0.01989670216128324 0.2143593231519945 chr21 48129895 978432 0.020328986797083184 0.2595133408244378 chr22 51304566 200355 0.0039052079692088225 0.07556430415935067 chrMT 16571 30627 1.8482288335043147 2.232944030783602 chrX 155270560 9765158 0.06289123965290007 0.39178317875181856 chrY 59373566 358489 0.006037855297423099 0.15026628197052727