BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231866.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 = 4,133,536 number of mapped reads = 3,355,297 (81.17%) number of supplementary alignments = 26,269 (0.64%) number of secondary alignments = 0 number of mapped bases = 213,344,442 bp number of sequenced bases = 213,260,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,618 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3709 >>>>>>> ACTG content number of A's = 63,043,210 bp (29.56%) number of C's = 42,184,541 bp (19.78%) number of T's = 60,718,375 bp (28.47%) number of G's = 47,298,056 bp (22.18%) number of N's = 16,299 bp (0.01%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,321,357 number of insertions = 15,519 mapped reads with insertion percentage = 0.46% number of deletions = 50,380 mapped reads with deletion percentage = 1.48% homopolymer indels = 43.67% >>>>>>> Coverage mean coverageData = 0.0689X std coverageData = 5.2435X There is a 5.72% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 20244425 0.08122116173182975 1.5703781037970328 chr2 243199373 18336064 0.07539519437823551 18.53998350444368 chr3 198022430 21378426 0.1079596185139229 0.3756904276171468 chr4 191154276 7354496 0.03847413803079142 0.26246556050375414 chr5 180915260 5325565 0.029436792672989553 0.2105204524674563 chr6 171115067 18592986 0.10865779575097265 0.49430694334491865 chr7 159138663 14319258 0.08997975557957276 1.3149800721785898 chr8 146364022 11793977 0.08057975477060886 1.050165417265938 chr9 141213431 9595662 0.06795148260366253 0.5436884687957316 chr10 135534747 10429252 0.07694891701830528 0.5682430288070753 chr11 135006516 8488803 0.06287698735963233 0.5047521726541148 chr12 133851895 6243846 0.046647423258370756 0.26333989760318066 chr13 115169878 8108854 0.07040776755880561 0.30576645771806094 chr14 107349540 8630232 0.08039374924196228 0.40509663680750957 chr15 102531392 3940186 0.0384290696063114 0.2272509625737451 chr16 90354753 5008267 0.05542892690991032 0.3413911280643645 chr17 81195210 5569377 0.06859243297726553 0.3471361109744676 chr18 78077248 4270832 0.054700083691474374 1.1566034467174295 chr19 59128983 5755778 0.0973427532146122 0.9068568971372298 chr20 63025520 5715675 0.09068826405557621 0.364000297417816 chr21 48129895 4260611 0.08852317255211133 0.36135126598308565 chr22 51304566 2301069 0.044851154183820595 0.23784908717279565 chrMT 16571 158045 9.537444933920705 6.600598189997767 chrX 155270560 7037612 0.04532483170022701 0.32002888869601775 chrY 59373566 485144 0.008171043659395496 0.16526065579432017