BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818771.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,448,941
number of mapped reads = 2,379,758 (97.17%)
number of supplementary alignments = 16,796 (0.69%)
number of secondary alignments = 0
number of mapped bases = 161,965,548 bp
number of sequenced bases = 161,896,709 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,179,914
duplication rate = 41.81%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.5641
>>>>>>> ACTG content
number of A's = 44,334,606 bp (27.38%)
number of C's = 35,572,544 bp (21.97%)
number of T's = 48,095,952 bp (29.71%)
number of G's = 33,883,700 bp (20.93%)
number of N's = 9,907 bp (0.01%)
GC percentage = 42.9%
>>>>>>> Mismatches and indels
general error rate = 0.0055
number of mismatches = 844,475
number of insertions = 21,226
mapped reads with insertion percentage = 0.88%
number of deletions = 42,027
mapped reads with deletion percentage = 1.75%
homopolymer indels = 40.07%
>>>>>>> Coverage
mean coverageData = 0.0523X
std coverageData = 0.6244X
There is a 2.23% of reference with a coverageData >= 1X
There is a 1.15% of reference with a coverageData >= 2X
There is a 0.68% of reference with a coverageData >= 3X
There is a 0.41% of reference with a coverageData >= 4X
There is a 0.25% of reference with a coverageData >= 5X
There is a 0.16% of reference with a coverageData >= 6X
There is a 0.1% of reference with a coverageData >= 7X
There is a 0.06% of reference with a coverageData >= 8X
There is a 0.04% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% 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 13426777 0.05386857993023817 0.9238778976784519
chr2 243199373 14245074 0.058573646075970764 1.003137239630202
chr3 198022430 11465326 0.05789912789172418 0.4698591174680014
chr4 191154276 9830149 0.05142521112109467 0.5078820378421822
chr5 180915260 10118732 0.05593078217945794 0.4838015018454256
chr6 171115067 9630812 0.056282665044335344 0.5120446056269758
chr7 159138663 8932544 0.0561305708594523 0.561377835188353
chr8 146364022 8310802 0.056781727411125665 0.5451034273384009
chr9 141213431 7013518 0.04966608310791627 0.5344801338477901
chr10 135534747 7735928 0.05707708297120295 0.6416563390955415
chr11 135006516 7552554 0.055942144303612724 0.5171755380312493
chr12 133851895 7383803 0.055163978066952286 0.4884614702430075
chr13 115169878 5139252 0.04462323039015462 0.41745381164763457
chr14 107349540 4992561 0.046507521131436615 0.47262591157525446
chr15 102531392 4761458 0.046439026205749745 0.4272314586425467
chr16 90354753 4921497 0.05446860111498506 0.6753838090476564
chr17 81195210 4369767 0.05381803926610942 0.4900266839907204
chr18 78077248 4323644 0.055376490728771585 0.6478501805819659
chr19 59128983 3296579 0.055752337225214915 0.8117765693416643
chr20 63025520 3580240 0.05680619533166882 0.5051568731540621
chr21 48129895 2212017 0.045959314891503504 0.4436678730831527
chr22 51304566 2016572 0.03930589725678607 0.4245233172429215
chrMT 16571 42058 2.5380483978033914 3.7851749874497003
chrX 155270560 5221303 0.03362712802736076 0.40508058093971405
chrY 59373566 1442581 0.024296687856006492 0.9650155738696935