BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716566.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,445,754
number of mapped reads = 2,306,100 (94.29%)
number of supplementary alignments = 64,952 (2.66%)
number of secondary alignments = 0
number of mapped bases = 176,729,500 bp
number of sequenced bases = 176,657,744 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 121,132
duplication rate = 3.95%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.1179
>>>>>>> ACTG content
number of A's = 43,724,173 bp (24.75%)
number of C's = 37,510,883 bp (21.23%)
number of T's = 51,407,184 bp (29.1%)
number of G's = 44,008,612 bp (24.91%)
number of N's = 6,892 bp (0%)
GC percentage = 46.15%
>>>>>>> Mismatches and indels
general error rate = 0.0066
number of mismatches = 1,124,772
number of insertions = 15,006
mapped reads with insertion percentage = 0.64%
number of deletions = 34,447
mapped reads with deletion percentage = 1.47%
homopolymer indels = 39.5%
>>>>>>> Coverage
mean coverageData = 0.0571X
std coverageData = 0.4157X
There is a 4.63% of reference with a coverageData >= 1X
There is a 0.73% of reference with a coverageData >= 2X
There is a 0.16% of reference with a coverageData >= 3X
There is a 0.05% 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 14267229 0.05724049530051121 0.5845814309216745
chr2 243199373 14796049 0.06083917412073262 0.4979570132528681
chr3 198022430 11450663 0.05782508072444117 0.28372514153390654
chr4 191154276 11014686 0.05762197022472048 0.4505693571458565
chr5 180915260 10192616 0.056339172273251026 0.28197139490862555
chr6 171115067 10047857 0.05871988467269221 0.3065990680770551
chr7 159138663 9611915 0.06039962142952024 0.525894275303276
chr8 146364022 8959626 0.06121467473748433 0.41929517589996923
chr9 141213431 7274573 0.05151473870782164 0.36877625018082677
chr10 135534747 8696272 0.06416267556835444 0.5893128764091642
chr11 135006516 8036102 0.059523808465659536 0.40963932128725045
chr12 133851895 7980950 0.05962522981090406 0.29504042404184583
chr13 115169878 5107541 0.0443478892979291 0.24934478197510268
chr14 107349540 5371883 0.05004104349212861 0.3043513012471073
chr15 102531392 5250986 0.05121344690219362 0.2698840875066716
chr16 90354753 5700911 0.06309475495993 0.341973191487928
chr17 81195210 5199761 0.0640402432606554 0.3443468730179422
chr18 78077248 4641889 0.059452518101047826 0.6144800848794202
chr19 59128983 4038469 0.06829931439882875 0.4744219397366063
chr20 63025520 4114808 0.0652879658906424 0.3363816910222873
chr21 48129895 2363551 0.049107753091919275 0.36868043576860543
chr22 51304566 2484392 0.048424383903764044 0.27123264359354754
chrMT 16571 38304 2.311508056242834 2.2383100926459214
chrX 155270560 9460326 0.06092800850335054 0.3251705813086838
chrY 59373566 628141 0.01057947235306702 0.4532988850220402