BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3082323.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,104,331
number of mapped reads = 1,826,413 (86.79%)
number of supplementary alignments = 12,891 (0.61%)
number of secondary alignments = 0
number of mapped bases = 120,953,539 bp
number of sequenced bases = 120,908,419 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 66,955
duplication rate = 2.65%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.0652
>>>>>>> ACTG content
number of A's = 33,303,634 bp (27.54%)
number of C's = 22,902,228 bp (18.94%)
number of T's = 36,924,207 bp (30.54%)
number of G's = 27,776,007 bp (22.97%)
number of N's = 2,343 bp (0%)
GC percentage = 41.91%
>>>>>>> Mismatches and indels
general error rate = 0.0089
number of mismatches = 1,060,119
number of insertions = 10,223
mapped reads with insertion percentage = 0.55%
number of deletions = 27,751
mapped reads with deletion percentage = 1.5%
homopolymer indels = 46.24%
>>>>>>> Coverage
mean coverageData = 0.0391X
std coverageData = 0.3636X
There is a 3.45% of reference with a coverageData >= 1X
There is a 0.32% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% 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 9522964 0.03820638023605967 0.5465267925890148
chr2 243199373 10411112 0.04280895905105808 0.537848957891879
chr3 198022430 8085538 0.040831425005743036 0.22257158402240798
chr4 191154276 7855281 0.04109393294450813 0.23829400121466046
chr5 180915260 7313400 0.040424450651647625 0.22293898035778809
chr6 171115067 7067746 0.041304054189453696 0.26758268189668594
chr7 159138663 6695551 0.042073691419664626 0.4875286394663323
chr8 146364022 6225797 0.042536389168097606 0.4605262417842877
chr9 141213431 5033331 0.03564342969614555 0.37859375522770056
chr10 135534747 5623546 0.0414915445999984 0.325676114098272
chr11 135006516 5395344 0.03996358220221015 0.3437933379118823
chr12 133851895 5539708 0.04138684775437808 0.22702484077398818
chr13 115169878 3832629 0.03327805035966088 0.1992260953259169
chr14 107349540 3637986 0.033889162450067324 0.23310146754121133
chr15 102531392 3489620 0.0340346496027285 0.2121868138909548
chr16 90354753 3414664 0.037791747380461545 0.24682895370624666
chr17 81195210 3251182 0.0400415492490259 0.24520279787522958
chr18 78077248 3294334 0.04219326480359554 0.6983259244827049
chr19 59128983 2517785 0.042581232963198434 0.4618887782064569
chr20 63025520 2448641 0.03885157948716647 0.2243844341434649
chr21 48129895 1566831 0.03255421604389538 0.21797103946247062
chr22 51304566 1339146 0.026101887305702967 0.17647623846398824
chrMT 16571 6177 0.37275964033552594 0.6601890629175373
chrX 155270560 7054661 0.04543463358411279 0.2774533147899466
chrY 59373566 330565 0.0055675449913181905 0.1276278982474345