BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472476.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 9,313,242
number of mapped reads = 9,180,840 (98.58%)
number of supplementary alignments = 34,874 (0.37%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 4,611,271
number of mapped paired reads (second in pair) = 4,569,569
number of mapped paired reads (both in pair) = 9,114,212
number of mapped paired reads (singletons) = 66,628
number of mapped bases = 896,317,786 bp
number of sequenced bases = 896,223,365 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 5,250,993
duplication rate = 43.97%
>>>>>>> Insert size
mean insert size = 25,604.1719
std insert size = 1,586,934.2921
median insert size = 201
>>>>>>> Mapping quality
mean mapping quality = 55.0957
>>>>>>> ACTG content
number of A's = 237,266,695 bp (26.47%)
number of C's = 212,359,197 bp (23.69%)
number of T's = 235,352,838 bp (26.26%)
number of G's = 211,104,955 bp (23.55%)
number of N's = 139,680 bp (0.02%)
GC percentage = 47.25%
>>>>>>> Mismatches and indels
general error rate = 0.0061
number of mismatches = 5,378,544
number of insertions = 45,816
mapped reads with insertion percentage = 0.49%
number of deletions = 39,041
mapped reads with deletion percentage = 0.42%
homopolymer indels = 43.07%
>>>>>>> Coverage
mean coverageData = 0.2895X
std coverageData = 11.1889X
There is a 3.12% of reference with a coverageData >= 1X
There is a 1.5% of reference with a coverageData >= 2X
There is a 0.63% of reference with a coverageData >= 3X
There is a 0.49% of reference with a coverageData >= 4X
There is a 0.35% of reference with a coverageData >= 5X
There is a 0.32% of reference with a coverageData >= 6X
There is a 0.28% of reference with a coverageData >= 7X
There is a 0.27% of reference with a coverageData >= 8X
There is a 0.25% of reference with a coverageData >= 9X
There is a 0.24% of reference with a coverageData >= 10X
There is a 0.23% of reference with a coverageData >= 11X
There is a 0.22% of reference with a coverageData >= 12X
There is a 0.21% of reference with a coverageData >= 13X
There is a 0.2% of reference with a coverageData >= 14X
There is a 0.2% of reference with a coverageData >= 15X
There is a 0.19% of reference with a coverageData >= 16X
There is a 0.19% of reference with a coverageData >= 17X
There is a 0.18% of reference with a coverageData >= 18X
There is a 0.18% of reference with a coverageData >= 19X
There is a 0.17% of reference with a coverageData >= 20X
There is a 0.17% of reference with a coverageData >= 21X
There is a 0.16% of reference with a coverageData >= 22X
There is a 0.16% of reference with a coverageData >= 23X
There is a 0.16% of reference with a coverageData >= 24X
There is a 0.15% of reference with a coverageData >= 25X
There is a 0.15% of reference with a coverageData >= 26X
There is a 0.15% of reference with a coverageData >= 27X
There is a 0.14% of reference with a coverageData >= 28X
There is a 0.14% of reference with a coverageData >= 29X
There is a 0.14% of reference with a coverageData >= 30X
There is a 0.13% of reference with a coverageData >= 31X
There is a 0.13% of reference with a coverageData >= 32X
There is a 0.13% of reference with a coverageData >= 33X
There is a 0.13% of reference with a coverageData >= 34X
There is a 0.12% of reference with a coverageData >= 35X
There is a 0.12% of reference with a coverageData >= 36X
There is a 0.12% of reference with a coverageData >= 37X
There is a 0.12% of reference with a coverageData >= 38X
There is a 0.12% of reference with a coverageData >= 39X
There is a 0.11% of reference with a coverageData >= 40X
There is a 0.11% of reference with a coverageData >= 41X
There is a 0.11% of reference with a coverageData >= 42X
There is a 0.11% of reference with a coverageData >= 43X
There is a 0.11% of reference with a coverageData >= 44X
There is a 0.11% of reference with a coverageData >= 45X
There is a 0.1% of reference with a coverageData >= 46X
There is a 0.1% of reference with a coverageData >= 47X
There is a 0.1% of reference with a coverageData >= 48X
There is a 0.1% of reference with a coverageData >= 49X
There is a 0.1% of reference with a coverageData >= 50X
There is a 0.1% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 115006688 0.46140983536406116 20.827714449476282
chr2 243199373 57631267 0.23697128117184743 8.943674112848289
chr3 198022430 110078954 0.5558913401880787 14.410724314940579
chr4 191154276 46564850 0.24359826509975638 11.085557759816613
chr5 180915260 41514766 0.22947078096120802 7.5000343555683715
chr6 171115067 57982765 0.33885248106176413 10.161790262140835
chr7 159138663 43563211 0.27374372876313535 12.982871771180108
chr8 146364022 39134024 0.26737461478067337 10.062859915786337
chr9 141213431 49930501 0.3535818133333224 10.923450602538157
chr10 135534747 28119685 0.20747214734535935 9.35090594265758
chr11 135006516 39540942 0.29288173024182035 9.752247872884583
chr12 133851895 44227292 0.3304196178918498 11.509201218241346
chr13 115169878 18580734 0.16133327848102783 6.51612104507374
chr14 107349540 22384637 0.20852103325268093 9.03055241894955
chr15 102531392 18643764 0.18183469117438686 5.734860511349817
chr16 90354753 26660583 0.29506563976772754 8.453799139444238
chr17 81195210 28270024 0.3481735437349075 10.257630629650636
chr18 78077248 18196438 0.233056856717081 11.034238807705082
chr19 59128983 20204020 0.3416940216949106 9.948628157570694
chr20 63025520 19713701 0.31278918444465037 9.918711949997608
chr21 48129895 4084349 0.08486095803865767 3.7700171154813686
chr22 51304566 7807719 0.15218370622217134 5.400687086861987
chrMT 16571 2751 0.1660129141270895 0.5598724430164796
chrX 155270560 37172964 0.23940767650995784 8.321609458103074
chrY 59373566 1301157 0.021914752433768253 0.9786877497322792