BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238670.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 = 3,828,913
number of mapped reads = 3,551,179 (92.75%)
number of supplementary alignments = 26,495 (0.69%)
number of secondary alignments = 0
number of mapped bases = 222,260,579 bp
number of sequenced bases = 222,156,856 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 359,902
duplication rate = 8.57%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9761
>>>>>>> ACTG content
number of A's = 55,796,000 bp (25.12%)
number of C's = 39,892,301 bp (17.96%)
number of T's = 73,115,695 bp (32.91%)
number of G's = 53,341,134 bp (24.01%)
number of N's = 11,726 bp (0.01%)
GC percentage = 41.97%
>>>>>>> Mismatches and indels
general error rate = 0.0057
number of mismatches = 1,234,594
number of insertions = 14,533
mapped reads with insertion percentage = 0.41%
number of deletions = 59,768
mapped reads with deletion percentage = 1.67%
homopolymer indels = 43.06%
>>>>>>> Coverage
mean coverageData = 0.0718X
std coverageData = 0.6538X
There is a 5.58% of reference with a coverageData >= 1X
There is a 1.1% of reference with a coverageData >= 2X
There is a 0.25% of reference with a coverageData >= 3X
There is a 0.07% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% 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 17663385 0.0708659618545143 0.7473431358142174
chr2 243199373 27225749 0.11194826970215914 1.4698397891258899
chr3 198022430 11951589 0.060354723452287706 0.30955327690010787
chr4 191154276 11535211 0.060345032511854454 0.31373443609004936
chr5 180915260 10984849 0.06071820033312834 0.3151136887630752
chr6 171115067 15938296 0.0931437323400633 0.5903442252983471
chr7 159138663 15045264 0.09454185247239384 0.8814618728601599
chr8 146364022 13790309 0.09421925423721958 0.7007577438962692
chr9 141213431 9190882 0.06508504137966876 0.5852728499608
chr10 135534747 11491537 0.08478664884363565 0.4556377236752448
chr11 135006516 8856626 0.06560147067271924 0.4366511064281831
chr12 133851895 6166921 0.04607272089797459 0.2942672022370444
chr13 115169878 6102151 0.052983914769797705 0.3636028454425378
chr14 107349540 6238643 0.058115228067116075 0.3581228834721948
chr15 102531392 7541472 0.07355281005060382 0.38268866086284703
chr16 90354753 5134061 0.05682115029410794 0.36275763589861004
chr17 81195210 4304409 0.053013090304218684 0.31061502047765577
chr18 78077248 12507347 0.1601919550238246 1.1996962964114866
chr19 59128983 3079603 0.05208280007115969 0.5529253926720987
chr20 63025520 4412223 0.07000692735260257 0.3617465681259351
chr21 48129895 3596514 0.07472515782550533 0.36806235956505523
chr22 51304566 1844105 0.03594426663700849 0.228616152079251
chrMT 16571 40504 2.4442701104338904 2.309046107937481
chrX 155270560 7208609 0.04642611580714335 0.33708533070114494
chrY 59373566 410320 0.006910819538782629 0.19757349010395137