BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1006415.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,239,212
number of mapped reads = 3,349,772 (79.02%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 1,687,809
number of mapped paired reads (second in pair) = 1,661,963
number of mapped paired reads (both in pair) = 3,069,672
number of mapped paired reads (singletons) = 280,100
number of mapped bases = 129,698,449 bp
number of sequenced bases = 129,683,355 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 81,226
duplication rate = 1.96%
>>>>>>> Insert size
mean insert size = 72,366.4018
std insert size = 2,555,803.7651
median insert size = 140
>>>>>>> Mapping quality
mean mapping quality = 48.0033
>>>>>>> ACTG content
number of A's = 36,047,341 bp (27.8%)
number of C's = 28,101,153 bp (21.67%)
number of T's = 36,595,601 bp (28.22%)
number of G's = 28,933,898 bp (22.31%)
number of N's = 5,362 bp (0%)
GC percentage = 43.98%
>>>>>>> Mismatches and indels
general error rate = 0.0035
number of mismatches = 443,871
number of insertions = 3,593
mapped reads with insertion percentage = 0.11%
number of deletions = 11,330
mapped reads with deletion percentage = 0.34%
homopolymer indels = 44.07%
>>>>>>> Coverage
mean coverageData = 0.0419X
std coverageData = 0.275X
There is a 3.72% of reference with a coverageData >= 1X
There is a 0.37% of reference with a coverageData >= 2X
There is a 0.05% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0% 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 10627010 0.042635841617421684 0.35543151233458997
chr2 243199373 10827068 0.04451930885529051 0.27141498396147434
chr3 198022430 8745034 0.044161835606198754 0.22861916604343802
chr4 191154276 8290104 0.04336865579716354 0.25876887065333837
chr5 180915260 8004381 0.04424381337428363 0.22921292409347077
chr6 171115067 7728702 0.04516669475984835 0.24731915539769173
chr7 159138663 6794065 0.04269273645964966 0.29015080621213174
chr8 146364022 6535329 0.04465119850286705 0.4553068752884137
chr9 141213431 5417189 0.03836171220852215 0.2332049028189158
chr10 135534747 6189327 0.045665979662027185 0.328626085013289
chr11 135006516 5836093 0.04322823203585226 0.2562844980349787
chr12 133851895 5896586 0.04405306327564507 0.23035051839539383
chr13 115169878 3613200 0.031372786554484326 0.19238265647763683
chr14 107349540 3882132 0.036163471217482625 0.22422898540576694
chr15 102531392 3739696 0.03647366847413912 0.20871832848403807
chr16 90354753 4111590 0.04550496640724589 0.27517377403657733
chr17 81195210 3749021 0.04617293310775352 0.24232338843911633
chr18 78077248 3359456 0.04302733620939099 0.348799865892545
chr19 59128983 2648739 0.04479595057469532 0.29574070267796493
chr20 63025520 2875812 0.04562932602539416 0.23786950159908926
chr21 48129895 1746133 0.036279592963998776 0.2348760476629401
chr22 51304566 1613774 0.03145478318635421 0.19732176361673437
chrMT 16571 3661 0.22092812745157203 0.5356283417065506
chrX 155270560 7107794 0.045776829812425486 0.2444608619755745
chrY 59373566 356553 0.006005248194120596 0.1610919497162376