BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR617420.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000
number of mapped reads = 30,247,224 (94.52%)
number of supplementary alignments = 496,808 (1.55%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 15,250,878
number of mapped paired reads (second in pair) = 14,996,346
number of mapped paired reads (both in pair) = 29,702,096
number of mapped paired reads (singletons) = 545,128
number of mapped bases = 2,979,068,998 bp
number of sequenced bases = 2,978,405,733 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,429,708
duplication rate = 4.23%
>>>>>>> Insert size
mean insert size = 59,036.9315
std insert size = 2,317,484.416
median insert size = 210
>>>>>>> Mapping quality
mean mapping quality = 53.9139
>>>>>>> ACTG content
number of A's = 889,034,652 bp (29.85%)
number of C's = 599,001,698 bp (20.11%)
number of T's = 880,963,593 bp (29.58%)
number of G's = 609,124,760 bp (20.45%)
number of N's = 281,030 bp (0.01%)
GC percentage = 40.56%
>>>>>>> Mismatches and indels
general error rate = 0.0086
number of mismatches = 25,276,318
number of insertions = 245,351
mapped reads with insertion percentage = 0.8%
number of deletions = 293,164
mapped reads with deletion percentage = 0.95%
homopolymer indels = 45.14%
>>>>>>> Coverage
mean coverageData = 0.9623X
std coverageData = 2.9596X
There is a 29.68% of reference with a coverageData >= 1X
There is a 17.09% of reference with a coverageData >= 2X
There is a 10.97% of reference with a coverageData >= 3X
There is a 7.6% of reference with a coverageData >= 4X
There is a 5.53% of reference with a coverageData >= 5X
There is a 4.16% of reference with a coverageData >= 6X
There is a 3.22% of reference with a coverageData >= 7X
There is a 2.55% of reference with a coverageData >= 8X
There is a 2.06% of reference with a coverageData >= 9X
There is a 1.68% of reference with a coverageData >= 10X
There is a 1.4% of reference with a coverageData >= 11X
There is a 1.17% of reference with a coverageData >= 12X
There is a 0.99% of reference with a coverageData >= 13X
There is a 0.85% of reference with a coverageData >= 14X
There is a 0.73% of reference with a coverageData >= 15X
There is a 0.63% of reference with a coverageData >= 16X
There is a 0.55% of reference with a coverageData >= 17X
There is a 0.48% of reference with a coverageData >= 18X
There is a 0.42% of reference with a coverageData >= 19X
There is a 0.37% of reference with a coverageData >= 20X
There is a 0.33% of reference with a coverageData >= 21X
There is a 0.3% of reference with a coverageData >= 22X
There is a 0.26% of reference with a coverageData >= 23X
There is a 0.24% of reference with a coverageData >= 24X
There is a 0.21% of reference with a coverageData >= 25X
There is a 0.19% of reference with a coverageData >= 26X
There is a 0.17% of reference with a coverageData >= 27X
There is a 0.16% of reference with a coverageData >= 28X
There is a 0.14% of reference with a coverageData >= 29X
There is a 0.13% of reference with a coverageData >= 30X
There is a 0.12% of reference with a coverageData >= 31X
There is a 0.11% of reference with a coverageData >= 32X
There is a 0.1% of reference with a coverageData >= 33X
There is a 0.09% of reference with a coverageData >= 34X
There is a 0.09% of reference with a coverageData >= 35X
There is a 0.08% of reference with a coverageData >= 36X
There is a 0.07% of reference with a coverageData >= 37X
There is a 0.07% of reference with a coverageData >= 38X
There is a 0.06% of reference with a coverageData >= 39X
There is a 0.06% of reference with a coverageData >= 40X
There is a 0.05% of reference with a coverageData >= 41X
There is a 0.05% of reference with a coverageData >= 42X
There is a 0.05% of reference with a coverageData >= 43X
There is a 0.04% of reference with a coverageData >= 44X
There is a 0.04% of reference with a coverageData >= 45X
There is a 0.04% of reference with a coverageData >= 46X
There is a 0.04% of reference with a coverageData >= 47X
There is a 0.03% of reference with a coverageData >= 48X
There is a 0.03% of reference with a coverageData >= 49X
There is a 0.03% of reference with a coverageData >= 50X
There is a 0.03% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 191763162 0.7693588133527659 2.785258157357255
chr2 243199373 296966010 1.221080491848143 3.1467714266239706
chr3 198022430 251508615 1.2701016495959574 3.448576696147538
chr4 191154276 142707220 0.7465552065390365 2.2938581947624685
chr5 180915260 190245800 1.051574090543827 2.887100887720435
chr6 171115067 136196539 0.7959353982545558 2.6233828893278455
chr7 159138663 222647388 1.3990779098100126 3.2631436010169135
chr8 146364022 131791332 0.9004352995984218 3.291295800013149
chr9 141213431 119172759 0.8439194356803073 2.63254897144033
chr10 135534747 95661060 0.7058046893318065 2.438145213346762
chr11 135006516 221799270 1.64287825929824 3.8735336841525188
chr12 133851895 141953727 1.0605283324528203 2.816691989556126
chr13 115169878 129012491 1.1201929987283654 2.7865310022273824
chr14 107349540 86574531 0.8064732368671538 2.914108518781393
chr15 102531392 68405379 0.6671652229202155 2.3972008275139625
chr16 90354753 75286199 0.8332289835378113 3.3499148501278744
chr17 81195210 92250849 1.1361612218257702 3.7838054462530724
chr18 78077248 42553850 0.5450224116505745 2.031419836639813
chr19 59128983 42667274 0.7215966153180751 2.3492084962099113
chr20 63025520 101703271 1.6136839648447168 4.797309923203255
chr21 48129895 40699808 0.8456242840338629 2.555416614945914
chr22 51304566 24175158 0.47120870294468525 2.1155566743529977
chrMT 16571 183218 11.056544565807737 5.0996548591115545
chrX 155270560 130727655 0.8419345882439014 2.5928855387519723
chrY 59373566 2416433 0.04069880188769528 0.6261756100131477