BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472556.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 = 10,719,770
number of mapped reads = 10,252,335 (95.64%)
number of supplementary alignments = 44,714 (0.42%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 5,145,152
number of mapped paired reads (second in pair) = 5,107,183
number of mapped paired reads (both in pair) = 10,158,218
number of mapped paired reads (singletons) = 94,117
number of mapped bases = 1,002,044,478 bp
number of sequenced bases = 1,001,931,235 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 5,948,383
duplication rate = 43.98%
>>>>>>> Insert size
mean insert size = 36,439.7668
std insert size = 1,877,753.8505
median insert size = 217
>>>>>>> Mapping quality
mean mapping quality = 54.478
>>>>>>> ACTG content
number of A's = 271,487,260 bp (27.1%)
number of C's = 231,499,490 bp (23.11%)
number of T's = 268,632,065 bp (26.81%)
number of G's = 230,156,583 bp (22.97%)
number of N's = 155,837 bp (0.02%)
GC percentage = 46.08%
>>>>>>> Mismatches and indels
general error rate = 0.0058
number of mismatches = 5,662,925
number of insertions = 50,777
mapped reads with insertion percentage = 0.49%
number of deletions = 46,773
mapped reads with deletion percentage = 0.45%
homopolymer indels = 44.25%
>>>>>>> Coverage
mean coverageData = 0.3237X
std coverageData = 13.926X
There is a 3.43% of reference with a coverageData >= 1X
There is a 1.58% of reference with a coverageData >= 2X
There is a 0.68% of reference with a coverageData >= 3X
There is a 0.51% of reference with a coverageData >= 4X
There is a 0.38% of reference with a coverageData >= 5X
There is a 0.34% of reference with a coverageData >= 6X
There is a 0.3% of reference with a coverageData >= 7X
There is a 0.28% of reference with a coverageData >= 8X
There is a 0.27% of reference with a coverageData >= 9X
There is a 0.26% of reference with a coverageData >= 10X
There is a 0.24% of reference with a coverageData >= 11X
There is a 0.24% of reference with a coverageData >= 12X
There is a 0.23% of reference with a coverageData >= 13X
There is a 0.22% of reference with a coverageData >= 14X
There is a 0.21% of reference with a coverageData >= 15X
There is a 0.21% of reference with a coverageData >= 16X
There is a 0.2% of reference with a coverageData >= 17X
There is a 0.19% of reference with a coverageData >= 18X
There is a 0.19% of reference with a coverageData >= 19X
There is a 0.18% of reference with a coverageData >= 20X
There is a 0.18% of reference with a coverageData >= 21X
There is a 0.18% of reference with a coverageData >= 22X
There is a 0.17% of reference with a coverageData >= 23X
There is a 0.17% of reference with a coverageData >= 24X
There is a 0.16% of reference with a coverageData >= 25X
There is a 0.16% of reference with a coverageData >= 26X
There is a 0.16% of reference with a coverageData >= 27X
There is a 0.16% of reference with a coverageData >= 28X
There is a 0.15% of reference with a coverageData >= 29X
There is a 0.15% of reference with a coverageData >= 30X
There is a 0.15% of reference with a coverageData >= 31X
There is a 0.14% of reference with a coverageData >= 32X
There is a 0.14% of reference with a coverageData >= 33X
There is a 0.14% of reference with a coverageData >= 34X
There is a 0.14% of reference with a coverageData >= 35X
There is a 0.13% of reference with a coverageData >= 36X
There is a 0.13% of reference with a coverageData >= 37X
There is a 0.13% of reference with a coverageData >= 38X
There is a 0.13% of reference with a coverageData >= 39X
There is a 0.13% of reference with a coverageData >= 40X
There is a 0.12% of reference with a coverageData >= 41X
There is a 0.12% of reference with a coverageData >= 42X
There is a 0.12% of reference with a coverageData >= 43X
There is a 0.12% of reference with a coverageData >= 44X
There is a 0.12% of reference with a coverageData >= 45X
There is a 0.11% of reference with a coverageData >= 46X
There is a 0.11% of reference with a coverageData >= 47X
There is a 0.11% of reference with a coverageData >= 48X
There is a 0.11% of reference with a coverageData >= 49X
There is a 0.11% of reference with a coverageData >= 50X
There is a 0.11% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 136783378 0.5487784842871064 31.003877063071375
chr2 243199373 61959548 0.2547685351146033 8.19653272275968
chr3 198022430 113581473 0.5735788263986055 15.57330079481757
chr4 191154276 35882953 0.18771723945113317 11.527839117763305
chr5 180915260 52899791 0.2924009340063409 13.738914196149944
chr6 171115067 59356432 0.3468802194958086 14.634058279251134
chr7 159138663 43966454 0.2762776384516942 8.801014673200536
chr8 146364022 43309463 0.2959023837155828 9.931204151756392
chr9 141213431 58067991 0.41120728098448367 12.664748148177512
chr10 135534747 26986293 0.19910977514865616 8.368832571776208
chr11 135006516 49202044 0.3644419947849036 16.26186910401025
chr12 133851895 54026671 0.40363022876889415 11.603488054158591
chr13 115169878 19101695 0.16585669214653506 6.254836952347985
chr14 107349540 22179018 0.20660561749961853 7.142835476081115
chr15 102531392 21045452 0.2052586197210704 7.1829690383793885
chr16 90354753 41591608 0.46031455589281506 13.666025026219764
chr17 81195210 30496844 0.3755990531953794 9.533165227691658
chr18 78077248 17428824 0.2232253882718817 8.149708530619149
chr19 59128983 35421578 0.5990561007957806 18.575323678284217
chr20 63025520 19234432 0.3051848203711766 8.534020448155909
chr21 48129895 4683894 0.09731776892511401 5.309115719526816
chr22 51304566 9077072 0.17692522727899113 6.447327693682432
chrMT 16571 4018 0.2424717880634844 0.8852185777698548
chrX 155270560 45529436 0.2932264558072052 9.605048389818304
chrY 59373566 228116 0.0038420464756993037 0.22692100532435766