BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1506019.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 3,910,305
number of mapped reads = 2,893,279 (73.99%)
number of supplementary alignments = 146 (0%)
number of secondary alignments = 0
number of mapped bases = 134,752,409 bp
number of sequenced bases = 134,724,823 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 145,051
duplication rate = 3.82%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.266
>>>>>>> ACTG content
number of A's = 39,798,490 bp (29.54%)
number of C's = 27,479,106 bp (20.4%)
number of T's = 39,149,746 bp (29.06%)
number of G's = 27,859,812 bp (20.68%)
number of N's = 437,669 bp (0.32%)
GC percentage = 41.08%
>>>>>>> Mismatches and indels
general error rate = 0.008
number of mismatches = 1,074,746
number of insertions = 5,975
mapped reads with insertion percentage = 0.21%
number of deletions = 20,000
mapped reads with deletion percentage = 0.69%
homopolymer indels = 45.82%
>>>>>>> Coverage
mean coverageData = 0.0435X
std coverageData = 0.417X
There is a 3.51% of reference with a coverageData >= 1X
There is a 0.6% of reference with a coverageData >= 2X
There is a 0.13% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 13169978 0.05283829563658339 0.8541079836852838
chr2 243199373 8094284 0.03328250356961241 0.33319242843665164
chr3 198022430 8055634 0.04068041180991466 0.24255829428574574
chr4 191154276 5817901 0.03043563095601377 0.21419287216680694
chr5 180915260 9581077 0.052958921209852614 0.28096568029736174
chr6 171115067 9241807 0.05400931175745032 0.34227316975602884
chr7 159138663 8478299 0.05327617337089228 0.6470488252445575
chr8 146364022 8155949 0.05572372833536919 0.5002693571089688
chr9 141213431 6434492 0.04556572242763509 0.32586006412461616
chr10 135534747 3955420 0.029183807750790283 0.40416866822428765
chr11 135006516 6942024 0.0514199181319515 0.35324434009715705
chr12 133851895 4023086 0.030056249857351666 0.22345880001326304
chr13 115169878 4140587 0.035951996059247364 0.22524288432252715
chr14 107349540 4726808 0.04403193530219133 0.39488434689214685
chr15 102531392 4542634 0.0443048115449364 0.2514334145047196
chr16 90354753 4235087 0.04687176777518279 0.28956664654871345
chr17 81195210 2136879 0.02631779633305955 0.21166562544690984
chr18 78077248 3815936 0.048873853750583014 0.5233976588202541
chr19 59128983 3359115 0.05680995730976804 0.6053881458018605
chr20 63025520 3473786 0.055117133504015516 0.28553334081984866
chr21 48129895 1952736 0.04057220569461039 0.2581989435661525
chr22 51304566 925133 0.018032176707234986 0.15935043126192278
chrMT 16571 25721 1.5521694526582583 1.629270070353788
chrX 155270560 9072838 0.05843244205469472 0.32361828975607143
chrY 59373566 395198 0.006656127071767931 0.12554372752310944