BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063529.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 = 4,286,568 number of mapped reads = 4,037,294 (94.18%) number of supplementary alignments = 34,357 (0.8%) number of secondary alignments = 0 number of mapped bases = 258,549,663 bp number of sequenced bases = 258,449,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 602,322 duplication rate = 12.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6672 >>>>>>> ACTG content number of A's = 66,517,084 bp (25.74%) number of C's = 46,795,848 bp (18.11%) number of T's = 83,924,508 bp (32.47%) number of G's = 61,182,555 bp (23.67%) number of N's = 29,371 bp (0.01%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,387,994 number of insertions = 16,598 mapped reads with insertion percentage = 0.41% number of deletions = 57,428 mapped reads with deletion percentage = 1.41% homopolymer indels = 44.42% >>>>>>> Coverage mean coverageData = 0.0835X std coverageData = 0.9763X There is a 5.75% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 25974574 0.10421066914814227 2.3296507865717957 chr2 243199373 24423657 0.10042648012912435 1.5242127664826388 chr3 198022430 17682868 0.08929729829090573 0.40946903379717603 chr4 191154276 18000579 0.09416780715907187 0.47391705738627915 chr5 180915260 11796585 0.06520503024454653 0.3586978853480316 chr6 171115067 14505547 0.08477071747282196 0.5601394385112463 chr7 159138663 18015397 0.11320565763456238 0.8924603176075687 chr8 146364022 9628627 0.06578547698012835 0.8832043205358878 chr9 141213431 8837205 0.0625804849965015 0.7041433562567276 chr10 135534747 12627914 0.09317104491293292 0.6561374710422435 chr11 135006516 11203487 0.08298478719353072 0.5538250036640368 chr12 133851895 10306138 0.07699657894271875 0.4422638861733413 chr13 115169878 7312013 0.063488935883044 0.3849189077619638 chr14 107349540 5025988 0.046818905791305675 0.4160995832590913 chr15 102531392 5020412 0.04896463319253483 0.3346972552228106 chr16 90354753 5553766 0.061466229673606654 0.3946402872933286 chr17 81195210 7315216 0.09009418166416468 0.4599402140918529 chr18 78077248 5619323 0.07197132511637705 1.2992922600166819 chr19 59128983 5827280 0.0985520079044823 1.3442127931629888 chr20 63025520 4185701 0.06641279595947801 0.4072732441252402 chr21 48129895 3842786 0.07984197763157388 0.4366678962350321 chr22 51304566 2910901 0.05673765956815618 0.3203612858870133 chrMT 16571 536085 32.35079355500573 18.14457546481057 chrX 155270560 21633184 0.139325729230319 0.6270022149780595 chrY 59373566 764430 0.012874921475998257 0.5069463291790854