BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238504.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 = 3,584,737
number of mapped reads = 3,224,669 (89.96%)
number of supplementary alignments = 21,856 (0.61%)
number of secondary alignments = 0
number of mapped bases = 198,747,652 bp
number of sequenced bases = 198,636,361 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 654,173
duplication rate = 16.07%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.6398
>>>>>>> ACTG content
number of A's = 49,383,788 bp (24.86%)
number of C's = 35,467,582 bp (17.86%)
number of T's = 65,966,556 bp (33.21%)
number of G's = 47,804,946 bp (24.07%)
number of N's = 13,489 bp (0.01%)
GC percentage = 41.92%
>>>>>>> Mismatches and indels
general error rate = 0.0062
number of mismatches = 1,198,663
number of insertions = 13,324
mapped reads with insertion percentage = 0.41%
number of deletions = 64,999
mapped reads with deletion percentage = 1.99%
homopolymer indels = 42.49%
>>>>>>> Coverage
mean coverageData = 0.0642X
std coverageData = 0.796X
There is a 3.87% of reference with a coverageData >= 1X
There is a 1.4% of reference with a coverageData >= 2X
There is a 0.57% of reference with a coverageData >= 3X
There is a 0.25% of reference with a coverageData >= 4X
There is a 0.11% of reference with a coverageData >= 5X
There is a 0.05% of reference with a coverageData >= 6X
There is a 0.03% 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% 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 16665621 0.06686290663243724 1.2817161708390026
chr2 243199373 15961345 0.06563069963177906 1.7370701991915618
chr3 198022430 12068655 0.06094589890650266 0.3847338677636414
chr4 191154276 2320961 0.012141820986520856 0.2011530912783803
chr5 180915260 10605486 0.058621290431774525 0.37985699262269484
chr6 171115067 13580750 0.07936618462709658 0.6434988828786228
chr7 159138663 9936633 0.06244009351768903 0.8941328865520316
chr8 146364022 13731321 0.0938162316966119 0.6769980934938121
chr9 141213431 7030490 0.049786269975977 0.46003572276423443
chr10 135534747 6725340 0.049620781009020516 0.4913158535923873
chr11 135006516 4678480 0.034653734787141684 0.3414830703108214
chr12 133851895 7714744 0.05763641971598534 0.37388661402314743
chr13 115169878 7359935 0.06390503426599098 0.5140753932529736
chr14 107349540 5168364 0.04814519000267724 0.36415491313120135
chr15 102531392 6366522 0.062093392821585804 0.4796294271242773
chr16 90354753 5448053 0.0602962524838068 0.4459160431087127
chr17 81195210 9915057 0.12211381681259276 0.5664827420048838
chr18 78077248 17819521 0.22822936843265787 1.4730137951542444
chr19 59128983 4612293 0.0780039291391161 0.8677272403366756
chr20 63025520 4719003 0.07487447941722654 0.4502398144331841
chr21 48129895 4793435 0.09959371405235769 0.5132188561753479
chr22 51304566 602035 0.011734530606885944 0.15574791768587448
chrMT 16571 35036 2.114296059380846 2.272103597311319
chrX 155270560 10372659 0.06680377142969021 0.43395296853548215
chrY 59373566 515913 0.008689270912244012 0.3377183469598854