BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6063578.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 = 1,925,319
number of mapped reads = 1,654,149 (85.92%)
number of supplementary alignments = 13,764 (0.71%)
number of secondary alignments = 0
number of mapped bases = 108,772,033 bp
number of sequenced bases = 108,718,171 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 283,572
duplication rate = 12.52%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.6382
>>>>>>> ACTG content
number of A's = 30,449,146 bp (28.01%)
number of C's = 19,877,468 bp (18.28%)
number of T's = 34,766,955 bp (31.98%)
number of G's = 23,621,763 bp (21.73%)
number of N's = 2,839 bp (0%)
GC percentage = 40.01%
>>>>>>> Mismatches and indels
general error rate = 0.008
number of mismatches = 857,199
number of insertions = 7,615
mapped reads with insertion percentage = 0.46%
number of deletions = 30,395
mapped reads with deletion percentage = 1.81%
homopolymer indels = 48.77%
>>>>>>> Coverage
mean coverageData = 0.0351X
std coverageData = 0.422X
There is a 1.4% of reference with a coverageData >= 1X
There is a 0.8% of reference with a coverageData >= 2X
There is a 0.49% of reference with a coverageData >= 3X
There is a 0.3% of reference with a coverageData >= 4X
There is a 0.18% of reference with a coverageData >= 5X
There is a 0.11% of reference with a coverageData >= 6X
There is a 0.07% of reference with a coverageData >= 7X
There is a 0.04% of reference with a coverageData >= 8X
There is a 0.03% of reference with a coverageData >= 9X
There is a 0.02% of reference with a coverageData >= 10X
There is a 0.01% 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% 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 9066656 0.03637566062473321 0.4979578676288431
chr2 243199373 16654951 0.06848270533986944 0.5993926750336743
chr3 198022430 5589224 0.028225206609170488 0.3428257652858065
chr4 191154276 5793462 0.03030778134411181 0.35809622351276904
chr5 180915260 4479872 0.02476226715203571 0.31716699405677495
chr6 171115067 4382778 0.025613045518662596 0.3381440766477645
chr7 159138663 5047289 0.03171629637230269 0.4786491935483114
chr8 146364022 4981347 0.03403395815400591 0.4861675127960771
chr9 141213431 3393959 0.024034250679738814 0.35625102873242714
chr10 135534747 4440589 0.03276347282368853 0.40747265561459783
chr11 135006516 5256789 0.0389372984041748 0.43402073210106995
chr12 133851895 5290595 0.03952573850373953 0.4067681487825954
chr13 115169878 2104417 0.01827228643934137 0.2702437366534988
chr14 107349540 3026231 0.0281904421760913 0.33698159131062505
chr15 102531392 2667075 0.026012277293572684 0.32555822670680695
chr16 90354753 2712897 0.030024950652014954 0.34576151542757294
chr17 81195210 2755212 0.03393318398954815 0.39608406692482234
chr18 78077248 3415972 0.04375118344335087 0.5511319002336789
chr19 59128983 1569404 0.026542042842170988 0.38955910267873106
chr20 63025520 1782968 0.028289619823842788 0.3378177322131465
chr21 48129895 1874427 0.038945171187263136 0.40599550452422917
chr22 51304566 838024 0.016334296639406325 0.24572983656837497
chrMT 16571 93676 5.653008267455193 4.986304409164681
chrX 155270560 11288757 0.0727037823525593 0.5593576294851972
chrY 59373566 265462 0.0044710469302113335 0.15049713306283857