BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3124876.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 3,832,820
number of mapped reads = 3,786,491 (98.79%)
number of supplementary alignments = 44,212 (1.15%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 1,897,197
number of mapped paired reads (second in pair) = 1,889,294
number of mapped paired reads (both in pair) = 3,771,576
number of mapped paired reads (singletons) = 14,915
number of mapped bases = 511,459,400 bp
number of sequenced bases = 511,119,645 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 542,572
duplication rate = 13.9%
>>>>>>> Insert size
mean insert size = 73,940.2375
std insert size = 2,651,261.4608
median insert size = 168
>>>>>>> Mapping quality
mean mapping quality = 53.5208
>>>>>>> ACTG content
number of A's = 146,748,695 bp (28.71%)
number of C's = 105,666,323 bp (20.67%)
number of T's = 147,794,184 bp (28.92%)
number of G's = 110,888,144 bp (21.7%)
number of N's = 22,299 bp (0%)
GC percentage = 42.37%
>>>>>>> Mismatches and indels
general error rate = 0.0137
number of mismatches = 6,810,300
number of insertions = 90,613
mapped reads with insertion percentage = 2.28%
number of deletions = 181,849
mapped reads with deletion percentage = 4.63%
homopolymer indels = 46.5%
>>>>>>> Coverage
mean coverageData = 0.1652X
std coverageData = 1.5339X
There is a 8.55% of reference with a coverageData >= 1X
There is a 5.1% of reference with a coverageData >= 2X
There is a 1.15% of reference with a coverageData >= 3X
There is a 0.59% of reference with a coverageData >= 4X
There is a 0.2% of reference with a coverageData >= 5X
There is a 0.11% of reference with a coverageData >= 6X
There is a 0.06% of reference with a coverageData >= 7X
There is a 0.04% 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 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% 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% 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 38739274 0.15542297886591824 1.8018167253682857
chr2 243199373 44549455 0.18318079709851884 1.652380032214324
chr3 198022430 33690411 0.1701343176124038 0.6170054810188492
chr4 191154276 22364507 0.11699715783496259 0.7696362526762139
chr5 180915260 43446292 0.24014719377458818 0.7355108110466185
chr6 171115067 32718709 0.19120881389129807 1.248322248566763
chr7 159138663 41272363 0.2593484337618194 2.2115475837833882
chr8 146364022 28777738 0.19661756766973784 1.290994362172783
chr9 141213431 21834708 0.15462203450038686 2.0699045335518234
chr10 135534747 29005663 0.21400905407673798 3.7570249112897027
chr11 135006516 22788117 0.16879271960473374 0.9764250299800101
chr12 133851895 22431059 0.16758118366572247 0.6043902620526223
chr13 115169878 8795058 0.07636595742508297 0.39308269880030877
chr14 107349540 11072582 0.10314512758974095 0.49135560691595753
chr15 102531392 12653259 0.12340863371873464 0.5147656417027642
chr16 90354753 22051904 0.24405914761340777 2.8013989011782017
chr17 81195210 11813619 0.14549650157934194 1.7686868146662749
chr18 78077248 14827803 0.18991195745013964 1.866227742366972
chr19 59128983 8597111 0.14539588817213378 1.0678552697279895
chr20 63025520 14505508 0.23015292852799946 0.746499177342916
chr21 48129895 4889353 0.10158661264480215 0.5668501730879887
chr22 51304566 4370428 0.0851859462177304 0.4368590347409027
chrMT 16571 48934 2.952990163538712 2.4814934235022714
chrX 155270560 15301822 0.0985494094952707 0.5590045715931593
chrY 59373566 913723 0.015389390625451064 0.9045535331022905