BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472472.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 = 16,945,522
number of mapped reads = 16,774,887 (98.99%)
number of supplementary alignments = 58,131 (0.34%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 8,409,899
number of mapped paired reads (second in pair) = 8,364,988
number of mapped paired reads (both in pair) = 16,685,666
number of mapped paired reads (singletons) = 89,221
number of mapped bases = 1,642,427,988 bp
number of sequenced bases = 1,642,223,369 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,758,796
duplication rate = 44.62%
>>>>>>> Insert size
mean insert size = 29,325.426
std insert size = 1,620,902.554
median insert size = 216
>>>>>>> Mapping quality
mean mapping quality = 54.9248
>>>>>>> ACTG content
number of A's = 447,119,829 bp (27.23%)
number of C's = 376,944,330 bp (22.95%)
number of T's = 444,210,013 bp (27.05%)
number of G's = 373,691,884 bp (22.76%)
number of N's = 257,313 bp (0.02%)
GC percentage = 45.71%
>>>>>>> Mismatches and indels
general error rate = 0.0058
number of mismatches = 9,394,113
number of insertions = 74,318
mapped reads with insertion percentage = 0.44%
number of deletions = 79,357
mapped reads with deletion percentage = 0.47%
homopolymer indels = 42.98%
>>>>>>> Coverage
mean coverageData = 0.5306X
std coverageData = 21.4533X
There is a 5.44% of reference with a coverageData >= 1X
There is a 2.57% of reference with a coverageData >= 2X
There is a 1.08% of reference with a coverageData >= 3X
There is a 0.74% of reference with a coverageData >= 4X
There is a 0.5% of reference with a coverageData >= 5X
There is a 0.43% of reference with a coverageData >= 6X
There is a 0.37% of reference with a coverageData >= 7X
There is a 0.34% of reference with a coverageData >= 8X
There is a 0.32% of reference with a coverageData >= 9X
There is a 0.3% of reference with a coverageData >= 10X
There is a 0.29% of reference with a coverageData >= 11X
There is a 0.28% of reference with a coverageData >= 12X
There is a 0.27% of reference with a coverageData >= 13X
There is a 0.26% of reference with a coverageData >= 14X
There is a 0.25% of reference with a coverageData >= 15X
There is a 0.25% of reference with a coverageData >= 16X
There is a 0.24% of reference with a coverageData >= 17X
There is a 0.23% of reference with a coverageData >= 18X
There is a 0.23% of reference with a coverageData >= 19X
There is a 0.22% of reference with a coverageData >= 20X
There is a 0.22% of reference with a coverageData >= 21X
There is a 0.21% of reference with a coverageData >= 22X
There is a 0.21% of reference with a coverageData >= 23X
There is a 0.2% of reference with a coverageData >= 24X
There is a 0.2% of reference with a coverageData >= 25X
There is a 0.2% of reference with a coverageData >= 26X
There is a 0.19% of reference with a coverageData >= 27X
There is a 0.19% of reference with a coverageData >= 28X
There is a 0.19% of reference with a coverageData >= 29X
There is a 0.18% of reference with a coverageData >= 30X
There is a 0.18% of reference with a coverageData >= 31X
There is a 0.18% of reference with a coverageData >= 32X
There is a 0.17% of reference with a coverageData >= 33X
There is a 0.17% of reference with a coverageData >= 34X
There is a 0.17% of reference with a coverageData >= 35X
There is a 0.17% of reference with a coverageData >= 36X
There is a 0.16% of reference with a coverageData >= 37X
There is a 0.16% of reference with a coverageData >= 38X
There is a 0.16% of reference with a coverageData >= 39X
There is a 0.16% of reference with a coverageData >= 40X
There is a 0.16% of reference with a coverageData >= 41X
There is a 0.15% of reference with a coverageData >= 42X
There is a 0.15% of reference with a coverageData >= 43X
There is a 0.15% of reference with a coverageData >= 44X
There is a 0.15% of reference with a coverageData >= 45X
There is a 0.15% of reference with a coverageData >= 46X
There is a 0.14% of reference with a coverageData >= 47X
There is a 0.14% of reference with a coverageData >= 48X
There is a 0.14% of reference with a coverageData >= 49X
There is a 0.14% of reference with a coverageData >= 50X
There is a 0.14% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 194326943 0.7796447696714064 29.325331452713716
chr2 243199373 124828643 0.5132769935225121 18.439601947635328
chr3 198022430 140946453 0.7117701413925686 17.494678190948843
chr4 191154276 77634395 0.4061347547360123 19.571851177076095
chr5 180915260 96707756 0.534547257097052 24.994093029452717
chr6 171115067 86015621 0.5026770728494645 14.701444668973924
chr7 159138663 63028059 0.39605748729961365 14.604275539510214
chr8 146364022 49062013 0.33520541680659743 11.550655639163036
chr9 141213431 91023397 0.6445803090783907 17.16089156991718
chr10 135534747 45558094 0.3361358987891127 15.893186636145948
chr11 135006516 72474461 0.5368219486532043 18.904166203588137
chr12 133851895 100713809 0.7524272181578004 30.76631079610257
chr13 115169878 26903585 0.23359914473470225 8.166546452255746
chr14 107349540 37833990 0.35243737420765847 18.810036535407743
chr15 102531392 55239732 0.5387592123980917 27.107097378621003
chr16 90354753 64959517 0.7189385709460132 21.68006008101876
chr17 81195210 69412011 0.8548781510633447 28.526051470708488
chr18 78077248 25804485 0.33049941770488633 9.754371058962324
chr19 59128983 23320324 0.3943975156819457 11.394034529149357
chr20 63025520 49908356 0.7918753546182562 34.395525154523476
chr21 48129895 5860468 0.12176357334666947 4.4920483244142675
chr22 51304566 13594016 0.2649669816912592 12.903686189833538
chrMT 16571 2696 0.16269386277231307 0.5256502382137054
chrX 155270560 123602313 0.796044742802499 36.792719334908114
chrY 59373566 3666851 0.06175898210324777 3.2650291883211695