BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081254.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,096,539 number of mapped reads = 4,413,268 (86.59%) number of supplementary alignments = 48,027 (0.94%) number of secondary alignments = 0 number of mapped bases = 298,540,664 bp number of sequenced bases = 298,423,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 268,072 duplication rate = 4.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1991 >>>>>>> ACTG content number of A's = 83,059,279 bp (27.83%) number of C's = 54,524,365 bp (18.27%) number of T's = 95,655,768 bp (32.05%) number of G's = 65,103,725 bp (21.82%) number of N's = 80,558 bp (0.03%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,540,675 number of insertions = 25,189 mapped reads with insertion percentage = 0.57% number of deletions = 71,575 mapped reads with deletion percentage = 1.6% homopolymer indels = 48.76% >>>>>>> Coverage mean coverageData = 0.0964X std coverageData = 0.7414X There is a 7.16% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.13% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 24514251 0.09835181513950972 1.2716351693365149 chr2 243199373 24952025 0.10259905151975865 0.7948999831149663 chr3 198022430 20373064 0.10288260779347067 0.4109568225938332 chr4 191154276 20793216 0.1087771429188432 0.45760340450945136 chr5 180915260 18212910 0.10067094395464485 0.40432248542610477 chr6 171115067 17453315 0.10199753479335633 0.5494216759712516 chr7 159138663 16378054 0.1029168757060627 1.0678290739329264 chr8 146364022 15285017 0.1044315180133544 1.201205425754534 chr9 141213431 12127305 0.08587926030916988 0.6609672788149881 chr10 135534747 14103334 0.10405696186528463 0.7405708293292822 chr11 135006516 13908152 0.10301837579454313 0.7960779813887149 chr12 133851895 12464707 0.09312312687093448 0.40303886949173806 chr13 115169878 9045388 0.07853952923350323 0.35476706791546786 chr14 107349540 8473879 0.07893726419321405 0.4057213693185177 chr15 102531392 8403476 0.081960030348559 0.3641938893524706 chr16 90354753 8467781 0.09371705105541045 0.4552228260656271 chr17 81195210 7890283 0.09717670537461508 0.5680548038570566 chr18 78077248 7960140 0.10195210773822357 1.3260856172647346 chr19 59128983 5597365 0.09466364405421956 0.9758369492817837 chr20 63025520 6360848 0.10092495865166999 0.43007219173274897 chr21 48129895 4166417 0.08656609369291166 0.43131983507125515 chr22 51304566 3234811 0.06305113271984408 0.3161585022658319 chrMT 16571 159282 9.61209341620904 5.794664196348606 chrX 155270560 17493322 0.11266348237553854 0.492237367317711 chrY 59373566 722322 0.01216571697916881 0.25490700940724864