BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3080689.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 = 3,037,567
number of mapped reads = 2,723,899 (89.67%)
number of supplementary alignments = 30,288 (1%)
number of secondary alignments = 0
number of mapped bases = 192,699,390 bp
number of sequenced bases = 192,625,814 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 146,206
duplication rate = 4.47%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 48.2905
>>>>>>> ACTG content
number of A's = 58,855,277 bp (30.55%)
number of C's = 35,385,624 bp (18.37%)
number of T's = 60,297,243 bp (31.3%)
number of G's = 38,084,769 bp (19.77%)
number of N's = 2,901 bp (0%)
GC percentage = 38.14%
>>>>>>> Mismatches and indels
general error rate = 0.0081
number of mismatches = 1,531,165
number of insertions = 15,130
mapped reads with insertion percentage = 0.55%
number of deletions = 40,255
mapped reads with deletion percentage = 1.46%
homopolymer indels = 47.76%
>>>>>>> Coverage
mean coverageData = 0.0622X
std coverageData = 0.5632X
There is a 4% of reference with a coverageData >= 1X
There is a 1.36% of reference with a coverageData >= 2X
There is a 0.49% of reference with a coverageData >= 3X
There is a 0.18% of reference with a coverageData >= 4X
There is a 0.07% of reference with a coverageData >= 5X
There is a 0.03% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% 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 15445764 0.06196880849496459 0.5709676028548094
chr2 243199373 16637979 0.06841291897574095 0.45229224430605924
chr3 198022430 13440786 0.06787506849602845 0.3729209038061765
chr4 191154276 13959016 0.0730248691899521 0.4219975946118277
chr5 180915260 12552269 0.06938203554526025 0.3784794005651812
chr6 171115067 12472395 0.07288893502288726 0.41920836361237873
chr7 159138663 10979553 0.06899362350430203 0.5503214204750958
chr8 146364022 10052363 0.06868056003544368 1.7160547273217301
chr9 141213431 7493819 0.053067324736271015 0.39847006326239315
chr10 135534747 8788057 0.064839881982441 0.45425744881454483
chr11 135006516 8831915 0.06541843506279356 0.3896250151444933
chr12 133851895 8447008 0.06310712298843435 0.36131513782514607
chr13 115169878 6331240 0.05497305467320197 0.3385883168633226
chr14 107349540 5782515 0.05386622988789705 0.3477160367664694
chr15 102531392 5277202 0.05146913444811127 0.3202541835141234
chr16 90354753 4317452 0.04778334129251618 0.33282768143562985
chr17 81195210 3847769 0.04738911322478259 0.3247960995898755
chr18 78077248 4802176 0.061505446503442335 0.5955013619968866
chr19 59128983 2699851 0.045660365915645804 0.43619622846024136
chr20 63025520 3434241 0.0544896892560347 0.341426218201753
chr21 48129895 2646080 0.05497788848282341 0.3584023970704405
chr22 51304566 1514932 0.02952821002325602 0.23367458899901833
chrMT 16571 580594 35.03675095045561 19.277084407273854
chrX 155270560 11862771 0.07640064542821254 0.40451831655155013
chrY 59373566 501643 0.00844892826548434 0.22980260140759068