BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549079.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,444,203
number of mapped reads = 6,570,910 (88.27%)
number of secondary alignments = 0
number of mapped bases = 261,087,535 bp
number of sequenced bases = 261,061,330 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 199,960
duplication rate = 1.96%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.4279
>>>>>>> ACTG content
number of A's = 78,553,907 bp (30.09%)
number of C's = 52,265,096 bp (20.02%)
number of T's = 79,457,631 bp (30.44%)
number of G's = 50,720,049 bp (19.43%)
number of N's = 64,647 bp (0.02%)
GC percentage = 39.45%
>>>>>>> Mismatches and indels
general error rate = 0.0039
number of mismatches = 1,019,453
number of insertions = 6,102
mapped reads with insertion percentage = 0.09%
number of deletions = 20,702
mapped reads with deletion percentage = 0.32%
homopolymer indels = 45.86%
>>>>>>> Coverage
mean coverageData = 0.0843X
std coverageData = 0.7063X
There is a 7.36% of reference with a coverageData >= 1X
There is a 0.81% of reference with a coverageData >= 2X
There is a 0.1% of reference with a coverageData >= 3X
There is a 0.02% 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 0.01% 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 20966796 0.08411933304671686 1.752951755940236
chr2 243199373 23044973 0.0947575345928215 0.4952629331048969
chr3 198022430 18688704 0.09437670267959039 0.34398756895074667
chr4 191154276 18464589 0.09659521819956568 0.3528631847443175
chr5 180915260 17151221 0.09480251140782707 0.35092236888355954
chr6 171115067 16134485 0.09429026492447916 0.432058420409811
chr7 159138663 14716236 0.09247429708517785 0.7077589997522697
chr8 146364022 14052753 0.0960123451649887 0.9981259206963349
chr9 141213431 11099103 0.07859806904627932 0.4691295822018748
chr10 135534747 12343309 0.09107117748926775 0.5266068744688435
chr11 135006516 12090077 0.08955180355887415 0.50859070523609
chr12 133851895 12092630 0.09034336047315579 0.352327761129444
chr13 115169878 9108668 0.07908897845667598 0.30462605335753296
chr14 107349540 8127191 0.07570773940903706 0.35851219386721733
chr15 102531392 7402485 0.07219725447597551 0.2934293392952167
chr16 90354753 6587916 0.07291167073413393 0.3584741563219846
chr17 81195210 5927139 0.07299862886000295 0.33999282441295303
chr18 78077248 7287804 0.09334094357424073 0.9831596352252707
chr19 59128983 4041647 0.06835306130666918 1.3016565737349683
chr20 63025520 5051840 0.08015546718218271 0.3261340208971808
chr21 48129895 3436221 0.07139473294092996 0.34676054257707983
chr22 51304566 2385056 0.046488181968053294 0.2787109465087328
chrMT 16571 3189 0.1924446321887635 0.49983787405183666
chrX 155270560 8736609 0.05626700257923975 0.338603842006492
chrY 59373566 2146894 0.03615908803591147 0.34136325020393965