BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1708583.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,106,023
number of mapped reads = 5,011,347 (98.15%)
number of supplementary alignments = 134 (0%)
number of secondary alignments = 0
number of mapped bases = 249,953,755 bp
number of sequenced bases = 249,932,556 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 48,943
duplication rate = 0.98%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.6906
>>>>>>> ACTG content
number of A's = 77,334,355 bp (30.94%)
number of C's = 47,530,742 bp (19.02%)
number of T's = 76,895,878 bp (30.77%)
number of G's = 48,162,676 bp (19.27%)
number of N's = 8,905 bp (0%)
GC percentage = 38.29%
>>>>>>> Mismatches and indels
general error rate = 0.0015
number of mismatches = 361,212
number of insertions = 15,671
mapped reads with insertion percentage = 0.31%
number of deletions = 12,568
mapped reads with deletion percentage = 0.25%
homopolymer indels = 48.66%
>>>>>>> Coverage
mean coverageData = 0.0807X
std coverageData = 0.296X
There is a 7.46% of reference with a coverageData >= 1X
There is a 0.57% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0% 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 19323665 0.0775270485685169 0.29194234276786807
chr2 243199373 22147386 0.09106678905788133 0.3130051701462474
chr3 198022430 19206218 0.09699011369570609 0.3226780783786035
chr4 191154276 19555880 0.10230417236389731 0.33133468537032107
chr5 180915260 17074171 0.094376621408277 0.31810838907727335
chr6 171115067 16087824 0.0940175770728594 0.31815504062791344
chr7 159138663 13930599 0.08753748923980843 0.30766361828422845
chr8 146364022 13547580 0.09256086171231342 0.31538877457032816
chr9 141213431 10468818 0.07413471881438813 0.28429444577204305
chr10 135534747 10236672 0.07552802677235233 0.28502907206905276
chr11 135006516 11474762 0.0849941346534711 0.30444171245105495
chr12 133851895 11560140 0.08636515754969326 0.30567669618407844
chr13 115169878 9563401 0.08303734592824696 0.30000710791165897
chr14 107349540 7608462 0.070875590151574 0.2777800403434506
chr15 102531392 6565518 0.06403422280661127 0.2641304037863704
chr16 90354753 4785433 0.05296271464545977 0.23896152091658915
chr17 81195210 4335656 0.05339792827680352 0.24155917518686615
chr18 78077248 7395445 0.09471959103886449 0.31839430493956344
chr19 59128983 2192897 0.037086668647759426 0.19898925674431253
chr20 63025520 3908013 0.062006834691724876 0.259110583217376
chr21 48129895 3255498 0.06763983175113929 0.27407436848926375
chr22 51304566 1556958 0.030347357387254772 0.1809754726877658
chrMT 16571 200 0.012069277653732424 0.10919528465391506
chrX 155270560 13825765 0.08904305491008727 0.31050000618099266
chrY 59373566 346794 0.005840882119157202 0.0801164815987626