BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3124942.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,141,120
number of mapped reads = 5,097,637 (99.15%)
number of supplementary alignments = 32,231 (0.63%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 2,551,335
number of mapped paired reads (second in pair) = 2,546,302
number of mapped paired reads (both in pair) = 5,080,282
number of mapped paired reads (singletons) = 17,355
number of mapped bases = 454,978,899 bp
number of sequenced bases = 454,745,163 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 338,607
duplication rate = 4.43%
>>>>>>> Insert size
mean insert size = 60,672.0366
std insert size = 2,309,398.9807
median insert size = 192
>>>>>>> Mapping quality
mean mapping quality = 53.2176
>>>>>>> ACTG content
number of A's = 129,336,356 bp (28.44%)
number of C's = 86,866,927 bp (19.1%)
number of T's = 135,224,708 bp (29.74%)
number of G's = 103,310,459 bp (22.72%)
number of N's = 6,713 bp (0%)
GC percentage = 41.82%
>>>>>>> Mismatches and indels
general error rate = 0.0075
number of mismatches = 3,308,779
number of insertions = 57,466
mapped reads with insertion percentage = 1.1%
number of deletions = 140,985
mapped reads with deletion percentage = 2.71%
homopolymer indels = 47.28%
>>>>>>> Coverage
mean coverageData = 0.147X
std coverageData = 1.3632X
There is a 9.88% of reference with a coverageData >= 1X
There is a 2.73% of reference with a coverageData >= 2X
There is a 0.81% of reference with a coverageData >= 3X
There is a 0.33% of reference with a coverageData >= 4X
There is a 0.16% of reference with a coverageData >= 5X
There is a 0.09% of reference with a coverageData >= 6X
There is a 0.06% of reference with a coverageData >= 7X
There is a 0.04% of reference with a coverageData >= 8X
There is a 0.03% of reference with a coverageData >= 9X
There is a 0.02% of reference with a coverageData >= 10X
There is a 0.02% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% 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 38937030 0.1562163811018148 1.8742263638727832
chr2 243199373 37413718 0.1538396976048125 1.2496439528926908
chr3 198022430 22816752 0.1152230684170475 0.47240828628229464
chr4 191154276 23867327 0.12485897516621601 0.9229515368180725
chr5 180915260 28396302 0.1569591310318433 0.5433009061999657
chr6 171115067 21931435 0.12816776093714763 0.8652956954934647
chr7 159138663 36694310 0.23058073574490193 2.126337419196877
chr8 146364022 36436903 0.2489471285504849 0.9978587121801502
chr9 141213431 19626242 0.13898282805691478 1.5681011719091575
chr10 135534747 21502386 0.15864851247333644 3.3912868914747443
chr11 135006516 21386355 0.158409798531502 0.9413473695246232
chr12 133851895 22420873 0.1675050846310394 0.5721836052956265
chr13 115169878 11473373 0.09962130028478454 0.41232790625122523
chr14 107349540 11628763 0.10832615584566083 0.498364521155131
chr15 102531392 11067321 0.10794080509508737 0.4497411043138144
chr16 90354753 16055247 0.17769122782063274 1.63457981872134
chr17 81195210 11449029 0.14100621206595806 1.989758396552812
chr18 78077248 8638730 0.1106433720614743 1.636942794754596
chr19 59128983 7003875 0.1184507942576993 1.228537886626578
chr20 63025520 8824417 0.14001339457413442 0.6023674400209261
chr21 48129895 3866124 0.08032687376525546 0.513828805024595
chr22 51304566 4285718 0.08353482612054451 0.42160056396636203
chrMT 16571 214638 12.952628085209101 7.903285511425552
chrX 155270560 24607487 0.15848134379112178 0.7598922828633815
chrY 59373566 4434544 0.07468886069602085 1.3151512968639472