BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6234074.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 = 3,063,502
number of mapped reads = 2,903,109 (94.76%)
number of supplementary alignments = 20,795 (0.68%)
number of secondary alignments = 0
number of mapped bases = 195,940,375 bp
number of sequenced bases = 195,855,761 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 226,000
duplication rate = 5.89%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6433
>>>>>>> ACTG content
number of A's = 54,412,053 bp (27.78%)
number of C's = 36,231,249 bp (18.5%)
number of T's = 62,255,309 bp (31.79%)
number of G's = 42,937,874 bp (21.92%)
number of N's = 19,276 bp (0.01%)
GC percentage = 40.42%
>>>>>>> Mismatches and indels
general error rate = 0.0063
number of mismatches = 1,208,553
number of insertions = 14,157
mapped reads with insertion percentage = 0.48%
number of deletions = 47,726
mapped reads with deletion percentage = 1.63%
homopolymer indels = 45.4%
>>>>>>> Coverage
mean coverageData = 0.0633X
std coverageData = 0.9403X
There is a 5.29% of reference with a coverageData >= 1X
There is a 0.7% 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 0.01% 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 15381583 0.06171131264704051 2.3813428181200975
chr2 243199373 12557753 0.05163563065600502 0.7878046727247201
chr3 198022430 21152568 0.10681905075096795 0.3740818859199648
chr4 191154276 6877210 0.03597727523500442 0.24473924322312263
chr5 180915260 12801496 0.07075962525217608 0.3236224414788842
chr6 171115067 13033926 0.07617053383148312 0.522162516446049
chr7 159138663 12366763 0.07771061266236728 1.4056234269057093
chr8 146364022 12821094 0.08759730584610471 1.3055480537229642
chr9 141213431 6968972 0.049350631527393454 0.5873595768615942
chr10 135534747 9013222 0.06650119028148553 0.7109414430318053
chr11 135006516 6029542 0.04466111843075782 0.45942150946940535
chr12 133851895 6898138 0.05153560209214819 0.2877084259852512
chr13 115169878 8392143 0.07286751662617894 0.31684883998493657
chr14 107349540 8837363 0.08232324982482458 0.39492159103723207
chr15 102531392 3731260 0.03639139123362336 0.23499934399673877
chr16 90354753 5444694 0.06025907679698931 0.39819367679605283
chr17 81195210 5360841 0.06602410413126587 0.3423292269931986
chr18 78077248 3843436 0.04922606903358069 1.4340088743954378
chr19 59128983 6529941 0.11043553717133947 1.2347872513870564
chr20 63025520 4575491 0.07259743354755344 0.3720291964072788
chr21 48129895 4008034 0.08327535308356687 0.3527157180099494
chr22 51304566 1404816 0.027381890337012108 0.1848185087557633
chrMT 16571 84010 5.069700078450305 3.3832030024594295
chrX 155270560 7403005 0.0476780981533138 0.3522446916970127
chrY 59373566 423074 0.0071256289372950915 0.13869244789491977