BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068098.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 = 2,387,099
number of mapped reads = 1,932,778 (80.97%)
number of supplementary alignments = 19,934 (0.84%)
number of secondary alignments = 0
number of mapped bases = 121,982,427 bp
number of sequenced bases = 121,937,960 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 298,117
duplication rate = 11.88%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.2069
>>>>>>> ACTG content
number of A's = 32,633,447 bp (26.76%)
number of C's = 21,835,191 bp (17.91%)
number of T's = 39,411,427 bp (32.32%)
number of G's = 28,055,549 bp (23.01%)
number of N's = 2,346 bp (0%)
GC percentage = 40.91%
>>>>>>> Mismatches and indels
general error rate = 0.0078
number of mismatches = 934,917
number of insertions = 9,260
mapped reads with insertion percentage = 0.47%
number of deletions = 28,244
mapped reads with deletion percentage = 1.45%
homopolymer indels = 46.63%
>>>>>>> Coverage
mean coverageData = 0.0394X
std coverageData = 0.4482X
There is a 2.1% of reference with a coverageData >= 1X
There is a 0.9% of reference with a coverageData >= 2X
There is a 0.43% of reference with a coverageData >= 3X
There is a 0.21% of reference with a coverageData >= 4X
There is a 0.11% of reference with a coverageData >= 5X
There is a 0.06% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% 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 10537221 0.04227560580480961 0.6551795483149586
chr2 243199373 10245375 0.04212747291910165 0.6815537773190633
chr3 198022430 8223229 0.04152675532766667 0.34994908157856347
chr4 191154276 8018595 0.04194828997704451 0.3705539920224075
chr5 180915260 7411114 0.04096455987184276 0.343725893391709
chr6 171115067 6635521 0.038778122326305724 0.3914736960838742
chr7 159138663 7048179 0.044289545149691245 0.5431238956784608
chr8 146364022 6018660 0.04112117115775898 0.4876095094983912
chr9 141213431 5343612 0.037840678200078574 0.3948265777276349
chr10 135534747 5874087 0.04334008163972889 0.42925586114788367
chr11 135006516 5268682 0.03902539044856176 0.39470778170738563
chr12 133851895 5393663 0.040295753750815407 0.3455578774543465
chr13 115169878 3533954 0.030684707332936483 0.30191352324056203
chr14 107349540 3614483 0.033670223458805694 0.3280062145211456
chr15 102531392 3388730 0.033050658280344036 0.3373721552212861
chr16 90354753 3251936 0.035990757453567494 0.3287051521912877
chr17 81195210 2945009 0.03627072335917353 0.32913605236793003
chr18 78077248 3268485 0.04186219524540619 0.5977701677001025
chr19 59128983 2482655 0.041987108082004385 0.48602821437328125
chr20 63025520 2474431 0.03926077880833034 0.341372912489364
chr21 48129895 1598162 0.03320518359742942 0.3168311538015831
chr22 51304566 1235553 0.024082710299118407 0.24961960358085852
chrMT 16571 162385 9.799348259006699 6.775759288161084
chrX 155270560 7672671 0.04941484721894479 0.40024590169814683
chrY 59373566 336035 0.0056596735321573916 0.1426825687838855