BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6004154.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 = 2,756,030
number of mapped reads = 2,410,507 (87.46%)
number of supplementary alignments = 28,578 (1.04%)
number of secondary alignments = 0
number of mapped bases = 160,236,776 bp
number of sequenced bases = 160,161,625 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 121,295
duplication rate = 4.3%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.5539
>>>>>>> ACTG content
number of A's = 44,346,481 bp (27.69%)
number of C's = 29,689,731 bp (18.54%)
number of T's = 50,634,110 bp (31.61%)
number of G's = 35,464,324 bp (22.14%)
number of N's = 26,979 bp (0.02%)
GC percentage = 40.68%
>>>>>>> Mismatches and indels
general error rate = 0.009
number of mismatches = 1,418,289
number of insertions = 10,833
mapped reads with insertion percentage = 0.45%
number of deletions = 44,357
mapped reads with deletion percentage = 1.82%
homopolymer indels = 45.6%
>>>>>>> Coverage
mean coverageData = 0.0518X
std coverageData = 0.3722X
There is a 4.15% of reference with a coverageData >= 1X
There is a 0.77% of reference with a coverageData >= 2X
There is a 0.16% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 10439257 0.04188257167872814 0.7436434514992706
chr2 243199373 24886155 0.10232820378200563 0.43874438884383477
chr3 198022430 10139732 0.051204967033280015 0.27000049745021704
chr4 191154276 13847330 0.07244059766677675 0.3219597250948683
chr5 180915260 16698505 0.09230014648847201 0.3613755637916379
chr6 171115067 7701969 0.04501046655348006 0.2989817993357258
chr7 159138663 8776315 0.055148854681530156 0.3150102614581715
chr8 146364022 9311597 0.06361943920890613 0.41881362513134607
chr9 141213431 5173119 0.03663333553590947 0.28214823295819585
chr10 135534747 1868178 0.013783756869373135 0.26257282284282135
chr11 135006516 8866191 0.06567231910495343 0.35725743752974415
chr12 133851895 760475 0.005681466071137805 0.10089577544686831
chr13 115169878 9648380 0.08377520379069951 0.3442767938576525
chr14 107349540 5773654 0.05378368645082224 0.2801420340703244
chr15 102531392 1731348 0.016886028427274255 0.15200987513112185
chr16 90354753 3804943 0.042111154905154796 0.2609371546544835
chr17 81195210 805117 0.009915818925771607 0.13972915666099195
chr18 78077248 3268396 0.04186105534867213 0.4431732832401472
chr19 59128983 3516562 0.059472729304341325 0.5634404900518775
chr20 63025520 1864760 0.02958737984232419 0.2146066381371902
chr21 48129895 435282 0.00904390088530216 0.130804637328017
chr22 51304566 1154164 0.022496321282593053 0.17596712867256858
chrMT 16571 74023 4.467020698811176 3.6053238501937037
chrX 155270560 9337642 0.06013787803689251 0.31255749101959973
chrY 59373566 353682 0.0059568933420640425 0.1182383923985838