BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6230379.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 = 3,469,242
number of mapped reads = 2,987,541 (86.12%)
number of supplementary alignments = 40,485 (1.17%)
number of secondary alignments = 0
number of mapped bases = 196,506,629 bp
number of sequenced bases = 196,414,392 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 732,520
duplication rate = 13.99%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.5763
>>>>>>> ACTG content
number of A's = 54,127,180 bp (27.56%)
number of C's = 36,173,982 bp (18.42%)
number of T's = 62,441,894 bp (31.79%)
number of G's = 43,524,839 bp (22.16%)
number of N's = 146,497 bp (0.07%)
GC percentage = 40.58%
>>>>>>> Mismatches and indels
general error rate = 0.0093
number of mismatches = 1,790,867
number of insertions = 16,927
mapped reads with insertion percentage = 0.56%
number of deletions = 54,875
mapped reads with deletion percentage = 1.82%
homopolymer indels = 46.1%
>>>>>>> Coverage
mean coverageData = 0.0635X
std coverageData = 0.8021X
There is a 1.77% of reference with a coverageData >= 1X
There is a 1.11% of reference with a coverageData >= 2X
There is a 0.85% of reference with a coverageData >= 3X
There is a 0.65% of reference with a coverageData >= 4X
There is a 0.49% of reference with a coverageData >= 5X
There is a 0.37% of reference with a coverageData >= 6X
There is a 0.28% of reference with a coverageData >= 7X
There is a 0.2% of reference with a coverageData >= 8X
There is a 0.15% of reference with a coverageData >= 9X
There is a 0.11% of reference with a coverageData >= 10X
There is a 0.08% of reference with a coverageData >= 11X
There is a 0.06% of reference with a coverageData >= 12X
There is a 0.04% of reference with a coverageData >= 13X
There is a 0.03% of reference with a coverageData >= 14X
There is a 0.02% of reference with a coverageData >= 15X
There is a 0.02% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% 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 32285464 0.12953012462103355 1.3650002652408117
chr2 243199373 14331994 0.05893104831318788 0.803984752119194
chr3 198022430 8443620 0.042639715107020956 0.5325982678021959
chr4 191154276 16500558 0.08632063245082731 0.7967541423881028
chr5 180915260 3208072 0.01773245662085111 0.3158036038140528
chr6 171115067 7758611 0.045341483576078076 0.5572972795752503
chr7 159138663 19065173 0.11980226954652748 0.9893750290371937
chr8 146364022 9871914 0.06744768191734989 1.4158963738252623
chr9 141213431 7252524 0.05135859916894166 0.675184497046535
chr10 135534747 7697384 0.0567926983329227 0.6853316045811272
chr11 135006516 8653682 0.06409825433907206 0.6724234574939496
chr12 133851895 10049116 0.07507638199668372 0.7127548057831912
chr13 115169878 5853480 0.05082474776955134 0.5925112956264837
chr14 107349540 964500 0.00898466821562533 0.262312101033385
chr15 102531392 9578888 0.09342395351464652 0.7853334756793009
chr16 90354753 5643819 0.06246289002638301 0.6409630143147657
chr17 81195210 4898356 0.06032814004668502 0.6087501727791167
chr18 78077248 6460492 0.0827448733848816 1.0910590557329736
chr19 59128983 4607030 0.07791492033610657 0.9326304340592668
chr20 63025520 4033162 0.06399252239410322 0.6530520038528036
chr21 48129895 3852941 0.08005296915773451 0.7596109199501648
chr22 51304566 3113493 0.06068646989431701 0.6082295673886745
chrMT 16571 12432 0.7502262989560075 1.8472896043063165
chrX 155270560 1888090 0.012159999938172439 0.2623441330489733
chrY 59373566 481834 0.008115294944554955 0.27969507269686794