BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237864.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 = 1,981,524 number of mapped reads = 1,757,581 (88.7%) number of supplementary alignments = 9,258 (0.47%) number of secondary alignments = 0 number of mapped bases = 111,875,205 bp number of sequenced bases = 111,833,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,862 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8932 >>>>>>> ACTG content number of A's = 30,291,802 bp (27.09%) number of C's = 19,880,512 bp (17.78%) number of T's = 35,435,673 bp (31.69%) number of G's = 26,139,247 bp (23.37%) number of N's = 86,007 bp (0.08%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 751,771 number of insertions = 8,045 mapped reads with insertion percentage = 0.45% number of deletions = 24,246 mapped reads with deletion percentage = 1.37% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.0361X std coverageData = 0.384X There is a 3.18% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 13464874 0.05402142608904473 0.8494278500685705 chr2 243199373 9485061 0.03900117374069052 0.32022748045586585 chr3 198022430 6053926 0.030571920564756223 0.20424541011120395 chr4 191154276 6029873 0.0315445363095095 0.2252134385258273 chr5 180915260 6001230 0.03317149697598754 0.2019774196599348 chr6 171115067 10029243 0.05861110407068946 0.3340434936392784 chr7 159138663 4840233 0.03041519206429427 0.42701992794678556 chr8 146364022 5637232 0.038515148210398316 0.3689127235295501 chr9 141213431 5191211 0.036761453660877345 0.33258626349367976 chr10 135534747 5674865 0.041870185510435934 0.5034273495544539 chr11 135006516 7167280 0.05308840056282913 0.39071708753395656 chr12 133851895 3724999 0.027829258599588746 0.18799928536241467 chr13 115169878 2794071 0.024260432054985768 0.1677793065487423 chr14 107349540 3464941 0.032277185351702486 0.22405270565866572 chr15 102531392 1061025 0.010348294110744151 0.11408101552597634 chr16 90354753 3466614 0.0383667032989399 0.25129788226002614 chr17 81195210 2340255 0.028822574632173498 0.2541298157776133 chr18 78077248 2395423 0.030680166903423647 0.5351872850527504 chr19 59128983 2188703 0.03701573896510278 0.5905457901569916 chr20 63025520 929321 0.014745154026495934 0.1516475480637223 chr21 48129895 1509658 0.03136632647962353 0.21944499378243001 chr22 51304566 1108020 0.021596908158232935 0.15881979097448903 chrMT 16571 92797 5.599963792167038 3.7687271586677187 chrX 155270560 6917174 0.04454916630686461 0.2741934083015647 chrY 59373566 307176 0.005173615477298433 0.13672893145963522