BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714135.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 705,416
number of mapped reads = 514,623 (72.95%)
number of supplementary alignments = 17,291 (2.45%)
number of secondary alignments = 0
number of mapped bases = 66,121,097 bp
number of sequenced bases = 64,858,396 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 430,771
duplication rate = 43.39%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 52.385
>>>>>>> ACTG content
number of A's = 18,161,396 bp (28%)
number of C's = 13,634,026 bp (21.02%)
number of T's = 17,239,425 bp (26.58%)
number of G's = 15,823,178 bp (24.4%)
number of N's = 371 bp (0%)
GC percentage = 45.42%
>>>>>>> Mismatches and indels
general error rate = 0.0429
number of mismatches = 2,540,185
number of insertions = 72,764
mapped reads with insertion percentage = 13.62%
number of deletions = 217,040
mapped reads with deletion percentage = 40.14%
homopolymer indels = 29.1%
>>>>>>> Coverage
mean coverageData = 0.0214X
std coverageData = 2.9522X
There is a 0.07% of reference with a coverageData >= 1X
There is a 0.05% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.03% of reference with a coverageData >= 5X
There is a 0.03% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.03% of reference with a coverageData >= 8X
There is a 0.03% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.02% of reference with a coverageData >= 13X
There is a 0.02% 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 0.02% of reference with a coverageData >= 17X
There is a 0.02% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.02% of reference with a coverageData >= 22X
There is a 0.02% of reference with a coverageData >= 23X
There is a 0.02% of reference with a coverageData >= 24X
There is a 0.02% of reference with a coverageData >= 25X
There is a 0.02% of reference with a coverageData >= 26X
There is a 0.02% of reference with a coverageData >= 27X
There is a 0.02% of reference with a coverageData >= 28X
There is a 0.02% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 5660434 0.02270980901588205 2.3831116227697797
chr2 243199373 7210931 0.02965028614609134 7.01428392371535
chr3 198022430 3539859 0.01787605070799303 1.6801264170975208
chr4 191154276 3494014 0.018278502961660142 2.0585634472810606
chr5 180915260 3557334 0.01966298475872074 1.8976118713575905
chr6 171115067 2651637 0.015496221615598584 1.4329367702069717
chr7 159138663 2791229 0.01753960318241457 1.9041585650352455
chr8 146364022 3248130 0.02219213407513494 2.5934247227678204
chr9 141213431 2706313 0.019164699709052463 2.291416393649396
chr10 135534747 3622554 0.026727861896551148 2.522136294190544
chr11 135006516 2980824 0.022079112092634107 2.1130014272807562
chr12 133851895 2521277 0.018836319052487078 1.933833706510882
chr13 115169878 2044827 0.017754876843752494 2.0597592057409977
chr14 107349540 2142617 0.01995925646258009 1.8666810908833884
chr15 102531392 1934427 0.018866680362634693 1.8090427558526454
chr16 90354753 2207638 0.024433003541053343 2.6426333134103923
chr17 81195210 2066148 0.025446673516824454 2.5603972219243523
chr18 78077248 1522224 0.019496383888940347 1.7742068067295989
chr19 59128983 1026802 0.01736546018388309 1.6149512905913583
chr20 63025520 1699027 0.026957762506362504 2.337431788656467
chr21 48129895 676926 0.014064564238089446 1.9895541283384317
chr22 51304566 665886 0.012979078704222933 1.4276378540896744
chrMT 16571 737218 44.48844366664655 406.27450057873244
chrX 155270560 5096474 0.032823182965270425 2.1856163918943956
chrY 59373566 316347 0.005328078155184413 0.8981990438479914