BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6231795.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 = 4,884,312
number of mapped reads = 4,408,700 (90.26%)
number of supplementary alignments = 23,383 (0.48%)
number of secondary alignments = 0
number of mapped bases = 275,874,411 bp
number of sequenced bases = 275,735,884 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 399,721
duplication rate = 7.43%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 37.5729
>>>>>>> ACTG content
number of A's = 64,413,150 bp (23.36%)
number of C's = 51,920,122 bp (18.83%)
number of T's = 87,984,770 bp (31.91%)
number of G's = 71,317,492 bp (25.86%)
number of N's = 100,350 bp (0.04%)
GC percentage = 44.69%
>>>>>>> Mismatches and indels
general error rate = 0.0076
number of mismatches = 2,052,650
number of insertions = 22,873
mapped reads with insertion percentage = 0.51%
number of deletions = 83,863
mapped reads with deletion percentage = 1.88%
homopolymer indels = 42.9%
>>>>>>> Coverage
mean coverageData = 0.0891X
std coverageData = 0.9035X
There is a 6.51% of reference with a coverageData >= 1X
There is a 1.49% of reference with a coverageData >= 2X
There is a 0.44% of reference with a coverageData >= 3X
There is a 0.17% of reference with a coverageData >= 4X
There is a 0.07% of reference with a coverageData >= 5X
There is a 0.04% 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 0.01% 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 29653072 0.11896889917879082 1.470422226000617
chr2 243199373 11577631 0.047605513357964126 2.100488113844912
chr3 198022430 19822092 0.10010023611971634 0.4259696470903479
chr4 191154276 3549022 0.018566270523815015 0.23961179552280867
chr5 180915260 16367653 0.09047137869961881 0.3976451990736052
chr6 171115067 19568911 0.11436112168895098 0.8038460889290024
chr7 159138663 6541293 0.041104360666898404 0.5417099005030513
chr8 146364022 13564405 0.09267581482558603 0.6170099958416636
chr9 141213431 7165149 0.05073985490799384 0.4984289828648804
chr10 135534747 6831004 0.050400389207942375 0.37145771473572214
chr11 135006516 8650298 0.06407318888223143 0.5624583070990784
chr12 133851895 8660513 0.06470220686827034 0.32975467494758526
chr13 115169878 12306459 0.10685484098541807 0.5279865065159244
chr14 107349540 17585461 0.16381496371572715 0.5625775013261588
chr15 102531392 6494594 0.06334249319466959 0.4306230994524856
chr16 90354753 8413974 0.09312154281468735 0.4828179097591926
chr17 81195210 14839574 0.18276415566878884 0.5850366001081337
chr18 78077248 6630977 0.08492841602204013 1.5896991033188588
chr19 59128983 28634720 0.484275537091514 1.2336665514440328
chr20 63025520 9565914 0.15177842245490397 0.5483843422542278
chr21 48129895 5966387 0.12396426379072716 0.480110487256341
chr22 51304566 5539434 0.10797155949043599 0.42626493775941815
chrMT 16571 281097 16.963188703156117 19.51678441819747
chrX 155270560 7100063 0.0457270393048109 0.39875638503483657
chrY 59373566 564714 0.009511202342133198 0.2839086063910126