BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR975297.sorted.bam
outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 71,037,568
number of mapped reads = 70,890,983 (99.79%)
number of supplementary alignments = 122,033 (0.17%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 35,460,278
number of mapped paired reads (second in pair) = 35,430,705
number of mapped paired reads (both in pair) = 70,822,420
number of mapped paired reads (singletons) = 68,563
number of mapped bases = 6,565,923,942 bp
number of sequenced bases = 6,563,913,665 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 45,918,450
duplication rate = 48.75%
>>>>>>> Insert size
mean insert size = 77,475.1885
std insert size = 2,743,162.9891
median insert size = 186
>>>>>>> Mapping quality
mean mapping quality = 56.2272
>>>>>>> ACTG content
number of A's = 1,761,440,992 bp (26.84%)
number of C's = 1,416,288,448 bp (21.58%)
number of T's = 1,858,555,201 bp (28.31%)
number of G's = 1,527,335,057 bp (23.27%)
number of N's = 293,967 bp (0%)
GC percentage = 44.85%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 33,881,044
number of insertions = 556,668
mapped reads with insertion percentage = 0.78%
number of deletions = 1,309,245
mapped reads with deletion percentage = 1.82%
homopolymer indels = 48.21%
>>>>>>> Coverage
mean coverageData = 2.121X
std coverageData = 31.1194X
There is a 11.54% of reference with a coverageData >= 1X
There is a 6% of reference with a coverageData >= 2X
There is a 3.7% of reference with a coverageData >= 3X
There is a 2.87% of reference with a coverageData >= 4X
There is a 2.38% of reference with a coverageData >= 5X
There is a 2.13% of reference with a coverageData >= 6X
There is a 1.95% of reference with a coverageData >= 7X
There is a 1.83% of reference with a coverageData >= 8X
There is a 1.74% of reference with a coverageData >= 9X
There is a 1.66% of reference with a coverageData >= 10X
There is a 1.6% of reference with a coverageData >= 11X
There is a 1.54% of reference with a coverageData >= 12X
There is a 1.49% of reference with a coverageData >= 13X
There is a 1.45% of reference with a coverageData >= 14X
There is a 1.41% of reference with a coverageData >= 15X
There is a 1.37% of reference with a coverageData >= 16X
There is a 1.34% of reference with a coverageData >= 17X
There is a 1.31% of reference with a coverageData >= 18X
There is a 1.28% of reference with a coverageData >= 19X
There is a 1.25% of reference with a coverageData >= 20X
There is a 1.22% of reference with a coverageData >= 21X
There is a 1.2% of reference with a coverageData >= 22X
There is a 1.18% of reference with a coverageData >= 23X
There is a 1.15% of reference with a coverageData >= 24X
There is a 1.13% of reference with a coverageData >= 25X
There is a 1.11% of reference with a coverageData >= 26X
There is a 1.09% of reference with a coverageData >= 27X
There is a 1.07% of reference with a coverageData >= 28X
There is a 1.06% of reference with a coverageData >= 29X
There is a 1.04% of reference with a coverageData >= 30X
There is a 1.02% of reference with a coverageData >= 31X
There is a 1.01% of reference with a coverageData >= 32X
There is a 0.99% of reference with a coverageData >= 33X
There is a 0.98% of reference with a coverageData >= 34X
There is a 0.96% of reference with a coverageData >= 35X
There is a 0.95% of reference with a coverageData >= 36X
There is a 0.93% of reference with a coverageData >= 37X
There is a 0.92% of reference with a coverageData >= 38X
There is a 0.91% of reference with a coverageData >= 39X
There is a 0.9% of reference with a coverageData >= 40X
There is a 0.88% of reference with a coverageData >= 41X
There is a 0.87% of reference with a coverageData >= 42X
There is a 0.86% of reference with a coverageData >= 43X
There is a 0.85% of reference with a coverageData >= 44X
There is a 0.84% of reference with a coverageData >= 45X
There is a 0.83% of reference with a coverageData >= 46X
There is a 0.82% of reference with a coverageData >= 47X
There is a 0.81% of reference with a coverageData >= 48X
There is a 0.8% of reference with a coverageData >= 49X
There is a 0.79% of reference with a coverageData >= 50X
There is a 0.78% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 762667121 3.0598404045701453 38.03481956923307
chr2 243199373 472258111 1.941855791708805 27.282317851183937
chr3 198022430 439157505 2.217715967832533 33.158996881052985
chr4 191154276 290065941 1.5174441664072427 24.328367393068426
chr5 180915260 312898055 1.7295282609106606 25.64184868635996
chr6 171115067 600583688 3.5098235271123146 52.566678329999164
chr7 159138663 342921235 2.1548580875032237 31.414028675256077
chr8 146364022 221661068 1.5144505116154843 23.063454942586514
chr9 141213431 259891333 1.840415116038077 27.199573271323278
chr10 135534747 297485634 2.1949030826759133 32.97260310344083
chr11 135006516 290956560 2.1551297568481806 28.122177932980303
chr12 133851895 363258288 2.713882295054545 32.78488830985918
chr13 115169878 137724460 1.1958375088319535 25.338625083758817
chr14 107349540 202998319 1.8910031566041177 25.919953367010372
chr15 102531392 235330831 2.295207608222075 31.615008379206994
chr16 90354753 194110436 2.1483146105219277 26.61329240081135
chr17 81195210 254157945 3.1302086046701523 36.275574168316645
chr18 78077248 124989444 1.6008433596430038 27.30520177156091
chr19 59128983 271034203 4.583779210273243 46.47354101036208
chr20 63025520 161894232 2.56870918320071 35.19661424952792
chr21 48129895 62864028 1.3061326645320959 21.13375755178751
chr22 51304566 103057008 2.008729749317049 28.049737194590037
chrMT 16571 178616 10.778830486995354 30.385780071567766
chrX 155270560 152211516 0.9802986219667141 17.511704963843176
chrY 59373566 11568365 0.19484032675416532 5.235657993672577