BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084346.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 = 2,268,312 number of mapped reads = 2,038,091 (89.85%) number of supplementary alignments = 10,700 (0.47%) number of secondary alignments = 0 number of mapped bases = 135,585,966 bp number of sequenced bases = 135,538,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,325 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6464 >>>>>>> ACTG content number of A's = 37,526,413 bp (27.69%) number of C's = 26,441,533 bp (19.51%) number of T's = 41,261,912 bp (30.44%) number of G's = 30,132,072 bp (22.23%) number of N's = 176,642 bp (0.13%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,364,406 number of insertions = 9,348 mapped reads with insertion percentage = 0.45% number of deletions = 27,382 mapped reads with deletion percentage = 1.33% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.0438X std coverageData = 0.2977X There is a 3.75% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% 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 13473322 0.05405531968564283 0.44014586769790465 chr2 243199373 12156965 0.04998764943361922 0.3359955838308424 chr3 198022430 8831882 0.04460041218562968 0.24030761524991454 chr4 191154276 6792406 0.03553363357668232 0.2203787897516461 chr5 180915260 6923338 0.038268402565930594 0.22043040545902023 chr6 171115067 6444904 0.037664152625437715 0.2460744635741213 chr7 159138663 7581179 0.04763882551910091 0.42912362876302246 chr8 146364022 6527420 0.04459716199927876 0.2822736083749755 chr9 141213431 4946969 0.035031858973811066 0.25931318256279423 chr10 135534747 9636470 0.07109962731549571 0.39596472472909466 chr11 135006516 7800859 0.057781351827492534 0.3234832811648562 chr12 133851895 6895693 0.05151733563428445 0.2577741202478337 chr13 115169878 3271846 0.028408869201024943 0.18978890989775615 chr14 107349540 3804841 0.03544347744759782 0.21743650981331883 chr15 102531392 3005186 0.029309911251375578 0.20074048529572483 chr16 90354753 3030460 0.0335395748356481 0.22269254811407177 chr17 81195210 3917993 0.04825399183030624 0.2680609790145872 chr18 78077248 3664513 0.046934453939770006 0.4030906490860544 chr19 59128983 2978763 0.05037737584629182 0.3367846053794441 chr20 63025520 2813272 0.044637029571513255 0.24234833273612066 chr21 48129895 1334734 0.027731911735938756 0.1966101468124371 chr22 51304566 1108216 0.0216007284809699 0.16462671406142348 chrMT 16571 4819 0.29080924506668276 0.6283003620894463 chrX 155270560 8361846 0.0538533898505937 0.288301634672034 chrY 59373566 278070 0.004683397321966479 0.10193191805506048