BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238617.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 = 4,356,829
number of mapped reads = 3,748,719 (86.04%)
number of supplementary alignments = 32,333 (0.74%)
number of secondary alignments = 0
number of mapped bases = 234,171,038 bp
number of sequenced bases = 234,080,533 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,668,498
duplication rate = 21.62%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9417
>>>>>>> ACTG content
number of A's = 58,970,700 bp (25.19%)
number of C's = 41,244,158 bp (17.62%)
number of T's = 78,680,090 bp (33.61%)
number of G's = 55,179,838 bp (23.57%)
number of N's = 5,747 bp (0%)
GC percentage = 41.19%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 1,186,295
number of insertions = 15,627
mapped reads with insertion percentage = 0.41%
number of deletions = 52,276
mapped reads with deletion percentage = 1.38%
homopolymer indels = 43.62%
>>>>>>> Coverage
mean coverageData = 0.0756X
std coverageData = 1.2784X
There is a 1.51% of reference with a coverageData >= 1X
There is a 0.91% of reference with a coverageData >= 2X
There is a 0.73% of reference with a coverageData >= 3X
There is a 0.62% of reference with a coverageData >= 4X
There is a 0.52% of reference with a coverageData >= 5X
There is a 0.45% of reference with a coverageData >= 6X
There is a 0.38% of reference with a coverageData >= 7X
There is a 0.33% of reference with a coverageData >= 8X
There is a 0.28% of reference with a coverageData >= 9X
There is a 0.24% of reference with a coverageData >= 10X
There is a 0.2% of reference with a coverageData >= 11X
There is a 0.17% of reference with a coverageData >= 12X
There is a 0.15% of reference with a coverageData >= 13X
There is a 0.13% of reference with a coverageData >= 14X
There is a 0.11% of reference with a coverageData >= 15X
There is a 0.09% of reference with a coverageData >= 16X
There is a 0.08% of reference with a coverageData >= 17X
There is a 0.07% of reference with a coverageData >= 18X
There is a 0.06% of reference with a coverageData >= 19X
There is a 0.05% of reference with a coverageData >= 20X
There is a 0.05% of reference with a coverageData >= 21X
There is a 0.04% of reference with a coverageData >= 22X
There is a 0.03% of reference with a coverageData >= 23X
There is a 0.03% of reference with a coverageData >= 24X
There is a 0.03% of reference with a coverageData >= 25X
There is a 0.02% of reference with a coverageData >= 26X
There is a 0.02% of reference with a coverageData >= 27X
There is a 0.02% of reference with a coverageData >= 28X
There is a 0.02% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% 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 13935046 0.055907768430394404 1.5363630037559113
chr2 243199373 12962436 0.05329962754468121 2.048620664279222
chr3 198022430 13850045 0.06994179901741435 0.9589126335731158
chr4 191154276 7605159 0.03978545057501094 0.6802645460832144
chr5 180915260 20634870 0.11405820603524545 1.2187058159979411
chr6 171115067 11662264 0.06815451265901676 1.210851385549575
chr7 159138663 17007674 0.10687329954506404 1.3724257034511484
chr8 146364022 23972529 0.16378703367416345 1.563465604850652
chr9 141213431 4546169 0.032193602037755176 0.6789431157618575
chr10 135534747 13951908 0.10293971331204094 1.2401391826554082
chr11 135006516 6130465 0.045408660127189714 0.7474711549167297
chr12 133851895 12162808 0.09086765637498072 1.071155281881139
chr13 115169878 9121177 0.07919759192590271 1.128288363422929
chr14 107349540 6022626 0.05610295116308835 0.867701397032376
chr15 102531392 7859522 0.076654786857863 1.0671995088228596
chr16 90354753 4766459 0.052752720158506766 0.8260125849955535
chr17 81195210 10461470 0.12884343793186814 1.2801163901989467
chr18 78077248 5490843 0.0703257753142119 2.5346145143248133
chr19 59128983 6222808 0.10524124861068555 1.4248597863647343
chr20 63025520 6214984 0.09861059456550299 1.1327144223878582
chr21 48129895 3573140 0.07423951371595554 0.9987311986497851
chr22 51304566 2326995 0.0453564893229971 0.7235065118578156
chrMT 16571 48488 2.926075674370889 5.8346278425621625
chrX 155270560 12982670 0.08361321038579368 1.0438649085546654
chrY 59373566 658483 0.011090507853275984 0.43164425468059925