BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004033.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 = 1,153,861 number of mapped reads = 964,392 (83.58%) number of supplementary alignments = 7,969 (0.69%) number of secondary alignments = 0 number of mapped bases = 63,949,248 bp number of sequenced bases = 63,918,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,622 duplication rate = 1.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.906 >>>>>>> ACTG content number of A's = 18,063,286 bp (28.26%) number of C's = 11,834,839 bp (18.52%) number of T's = 19,773,927 bp (30.94%) number of G's = 14,235,292 bp (22.27%) number of N's = 11,210 bp (0.02%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 647,920 number of insertions = 5,795 mapped reads with insertion percentage = 0.6% number of deletions = 18,525 mapped reads with deletion percentage = 1.9% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2486X There is a 1.9% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 4389689 0.017611546893598312 0.45739936982632173 chr2 243199373 5974158 0.024564857739168597 0.27558930854224556 chr3 198022430 4036384 0.020383468680795404 0.1504445675846141 chr4 191154276 4221041 0.0220818549724726 0.16273672034438696 chr5 180915260 4219624 0.023323759421952577 0.16306324875565548 chr6 171115067 3473380 0.02029850474826977 0.15881561123524848 chr7 159138663 3584527 0.022524551434744678 0.3454438926848516 chr8 146364022 4931449 0.03369304103982603 0.33989645260499596 chr9 141213431 2173656 0.015392700146206348 0.23480148651246938 chr10 135534747 2782751 0.02053164270856683 0.22509827059830542 chr11 135006516 1993777 0.014768005716109287 0.18069192828549385 chr12 133851895 2915051 0.02177818252031471 0.16064894239357877 chr13 115169878 2434837 0.02114126577437201 0.15326448984596933 chr14 107349540 1504583 0.014015737747921416 0.14468994667679225 chr15 102531392 2383537 0.023246899837271302 0.1618352244106218 chr16 90354753 1549090 0.01714453250732698 0.16939477554662666 chr17 81195210 1393163 0.017158191967235507 0.14816187968888625 chr18 78077248 1907198 0.02442706484736757 0.4367722553281567 chr19 59128983 867407 0.014669743262792124 0.33174323831234603 chr20 63025520 975356 0.015475572434785147 0.13756455954970284 chr21 48129895 793299 0.01648245856343547 0.14962144195127466 chr22 51304566 399056 0.007778177092463856 0.09148824133756142 chrMT 16571 32457 1.9586627240359664 2.010801095252422 chrX 155270560 4812245 0.03099264277787109 0.2089065067795988 chrY 59373566 201533 0.0033943219782352303 0.08726003759122725