BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3082915.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,172,508
number of mapped reads = 1,947,688 (89.65%)
number of supplementary alignments = 21,643 (1%)
number of secondary alignments = 0
number of mapped bases = 129,493,830 bp
number of sequenced bases = 129,445,770 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 94,888
duplication rate = 4.29%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.5973
>>>>>>> ACTG content
number of A's = 35,017,448 bp (27.05%)
number of C's = 24,184,230 bp (18.68%)
number of T's = 40,727,434 bp (31.46%)
number of G's = 29,510,968 bp (22.8%)
number of N's = 5,690 bp (0%)
GC percentage = 41.48%
>>>>>>> Mismatches and indels
general error rate = 0.0072
number of mismatches = 920,580
number of insertions = 10,227
mapped reads with insertion percentage = 0.52%
number of deletions = 29,600
mapped reads with deletion percentage = 1.51%
homopolymer indels = 48.13%
>>>>>>> Coverage
mean coverageData = 0.0418X
std coverageData = 0.2846X
There is a 3.45% of reference with a coverageData >= 1X
There is a 0.56% of reference with a coverageData >= 2X
There is a 0.11% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% 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 12509998 0.050190438642879046 0.33531145166356646
chr2 243199373 13148849 0.05406613034318966 0.4754882731763573
chr3 198022430 8944148 0.04516734796154153 0.24917377874050448
chr4 191154276 8455755 0.04423523855673519 0.2522536091863931
chr5 180915260 6134639 0.03390890851330065 0.21620526886825975
chr6 171115067 9670536 0.05651481292410095 0.3296378097881226
chr7 159138663 7145981 0.04490411610407962 0.274079658807147
chr8 146364022 10837484 0.0740447266473724 0.35055117455818663
chr9 141213431 3722357 0.02635979434562425 0.22300951915622721
chr10 135534747 4379789 0.032314879371855836 0.22155105000454314
chr11 135006516 4780347 0.035408268738673324 0.23412328258941623
chr12 133851895 4715202 0.03522700967363966 0.22081069474518442
chr13 115169878 2869857 0.02491846869890754 0.1877335331502441
chr14 107349540 2657355 0.02475422810381861 0.186991701185431
chr15 102531392 2370250 0.02311731025752581 0.19006934510844403
chr16 90354753 5211343 0.05767646777807029 0.29009151995729926
chr17 81195210 3366399 0.04146056152819852 0.24529216287279262
chr18 78077248 3774760 0.04834647860539347 0.36719001122695255
chr19 59128983 2210302 0.037381025139566496 0.2736829462604924
chr20 63025520 2272597 0.03605836175568246 0.22566347563589653
chr21 48129895 2767882 0.057508581724518615 0.2872749677012614
chr22 51304566 1685080 0.03284463998779368 0.21176760405066233
chrMT 16571 126379 7.6265162030052505 5.175082904264075
chrX 155270560 5519995 0.03555081529943603 0.22666958811967633
chrY 59373566 216546 0.003647178611437959 0.07387220357810127