BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3080718.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 = 2,392,970
number of mapped reads = 2,196,255 (91.78%)
number of supplementary alignments = 15,088 (0.63%)
number of secondary alignments = 0
number of mapped bases = 149,166,347 bp
number of sequenced bases = 149,111,167 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 118,860
duplication rate = 4.62%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.3356
>>>>>>> ACTG content
number of A's = 42,008,478 bp (28.17%)
number of C's = 27,630,406 bp (18.53%)
number of T's = 47,376,485 bp (31.77%)
number of G's = 32,093,542 bp (21.52%)
number of N's = 2,256 bp (0%)
GC percentage = 40.05%
>>>>>>> Mismatches and indels
general error rate = 0.0083
number of mismatches = 1,215,369
number of insertions = 10,715
mapped reads with insertion percentage = 0.48%
number of deletions = 31,289
mapped reads with deletion percentage = 1.41%
homopolymer indels = 48.26%
>>>>>>> Coverage
mean coverageData = 0.0482X
std coverageData = 0.3786X
There is a 3.92% of reference with a coverageData >= 1X
There is a 0.67% 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 18021161 0.0723013685089274 0.48641117133351747
chr2 243199373 10257002 0.04217528143051586 0.3800461033875854
chr3 198022430 9407588 0.04750768890170674 0.2569014934799348
chr4 191154276 6363126 0.033287908244333496 0.21924881153765544
chr5 180915260 6810359 0.037643916826032256 0.22677178945583762
chr6 171115067 8676919 0.0507080945712396 0.36265324063437704
chr7 159138663 9427332 0.05923973359007044 0.9396733441550142
chr8 146364022 17827129 0.12179993933208531 0.5259959323858976
chr9 141213431 4658172 0.03298674897290754 0.2747691231572999
chr10 135534747 6983620 0.05152641779749661 0.33144789810593944
chr11 135006516 6233601 0.04617259362503659 0.28016701030271995
chr12 133851895 4728473 0.03532615657028987 0.22164257763633666
chr13 115169878 3181858 0.027627519063621826 0.1953760451341917
chr14 107349540 2993325 0.027883910820670495 0.2075030390781396
chr15 102531392 2742863 0.02675144603518111 0.19261723115498777
chr16 90354753 3478419 0.03849735497589153 0.24626088591362216
chr17 81195210 2299420 0.028319650875956844 0.20891625990362545
chr18 78077248 4865221 0.06231291604950011 0.43132817185965117
chr19 59128983 2358050 0.03987976590092882 0.33740185389782185
chr20 63025520 3675830 0.058322882540278925 0.2881000877189985
chr21 48129895 2231163 0.046357113390752255 0.25950227729337855
chr22 51304566 1458703 0.02843222570092494 0.19595209850621792
chrMT 16571 70440 4.25079958964456 2.917733387124439
chrX 155270560 10108366 0.06510162647703467 0.3181722665965777
chrY 59373566 308207 0.005190980107207979 0.10205167579582498