BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524847.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 = 1,531,744
number of mapped reads = 1,403,304 (91.61%)
number of supplementary alignments = 8,551 (0.56%)
number of secondary alignments = 0
number of mapped bases = 81,700,884 bp
number of sequenced bases = 81,676,032 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 38,814
duplication rate = 1.83%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6525
>>>>>>> ACTG content
number of A's = 21,532,266 bp (26.36%)
number of C's = 14,252,536 bp (17.45%)
number of T's = 25,761,452 bp (31.54%)
number of G's = 20,119,187 bp (24.63%)
number of N's = 10,591 bp (0.01%)
GC percentage = 42.08%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 397,939
number of insertions = 5,691
mapped reads with insertion percentage = 0.4%
number of deletions = 16,114
mapped reads with deletion percentage = 1.14%
homopolymer indels = 42.99%
>>>>>>> Coverage
mean coverageData = 0.0264X
std coverageData = 0.2726X
There is a 2.42% of reference with a coverageData >= 1X
There is a 0.14% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% 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 6805098 0.02730223087388015 0.5474043116716909
chr2 243199373 5294113 0.021768612865626098 0.26966583729652416
chr3 198022430 5871415 0.02965025224667731 0.18249554460819928
chr4 191154276 4450040 0.023279834974761434 0.1742781392436702
chr5 180915260 4943794 0.02732657267275298 0.17568991324551744
chr6 171115067 5325470 0.03112215711548066 0.20531589331514577
chr7 159138663 3761013 0.023633559118188645 0.35898785459061705
chr8 146364022 8841802 0.06040966816284948 0.36816096802459614
chr9 141213431 3369090 0.023858141369003348 0.22990600598401223
chr10 135534747 4067877 0.030013535938499963 0.25034794925418796
chr11 135006516 3916167 0.02900724436144993 0.23426313247669894
chr12 133851895 3257600 0.02433734688627307 0.17116470289990837
chr13 115169878 2160758 0.01876148553356981 0.1455439207551381
chr14 107349540 1724852 0.016067623578079608 0.14314831404916958
chr15 102531392 2433363 0.02373285832303925 0.16541981596137337
chr16 90354753 2352856 0.026040201781083946 0.18307791621377761
chr17 81195210 2182543 0.02688019404100316 0.19445525440239314
chr18 78077248 1969052 0.025219280269714425 0.40131855007886974
chr19 59128983 1234703 0.020881519305008173 0.3597370800704057
chr20 63025520 1741419 0.027630378932216666 0.1799965482650742
chr21 48129895 1188801 0.024699846114353666 0.17990095285913837
chr22 51304566 491582 0.009581642304507556 0.10359522127376923
chrMT 16571 3222 0.19443606300162936 0.4340194473008923
chrX 155270560 4109234 0.026464991174115684 0.1996973606425644
chrY 59373566 205020 0.003453051817706216 0.09496023319234362