BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR5365351.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 557,871,970
number of mapped reads = 540,504,399 (96.89%)
number of supplementary alignments = 2,709,349 (0.49%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 270,736,777
number of mapped paired reads (second in pair) = 269,767,622
number of mapped paired reads (both in pair) = 538,179,174
number of mapped paired reads (singletons) = 2,325,225
number of mapped bases = 57,300,995,598 bp
number of sequenced bases = 57,280,341,829 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 289,925,203
duplication rate = 28.38%
>>>>>>> Insert size
mean insert size = 49,871.7397
std insert size = 2,161,178.1038
median insert size = 165
>>>>>>> Mapping quality
mean mapping quality = 53.6085
>>>>>>> ACTG content
number of A's = 17,260,205,041 bp (30.13%)
number of C's = 11,224,359,794 bp (19.6%)
number of T's = 16,829,577,492 bp (29.38%)
number of G's = 11,959,428,756 bp (20.88%)
number of N's = 6,770,746 bp (0.01%)
GC percentage = 40.47%
>>>>>>> Mismatches and indels
general error rate = 0.006
number of mismatches = 312,136,719
number of insertions = 17,447,205
mapped reads with insertion percentage = 3.15%
number of deletions = 9,471,361
mapped reads with deletion percentage = 1.7%
homopolymer indels = 49.73%
>>>>>>> Coverage
mean coverageData = 18.5099X
std coverageData = 226.4837X
There is a 86.64% of reference with a coverageData >= 1X
There is a 84.29% of reference with a coverageData >= 2X
There is a 81.39% of reference with a coverageData >= 3X
There is a 78.85% of reference with a coverageData >= 4X
There is a 75.97% of reference with a coverageData >= 5X
There is a 73.26% of reference with a coverageData >= 6X
There is a 70.34% of reference with a coverageData >= 7X
There is a 67.55% of reference with a coverageData >= 8X
There is a 64.63% of reference with a coverageData >= 9X
There is a 61.83% of reference with a coverageData >= 10X
There is a 58.96% of reference with a coverageData >= 11X
There is a 56.22% of reference with a coverageData >= 12X
There is a 53.45% of reference with a coverageData >= 13X
There is a 50.81% of reference with a coverageData >= 14X
There is a 48.18% of reference with a coverageData >= 15X
There is a 45.68% of reference with a coverageData >= 16X
There is a 43.22% of reference with a coverageData >= 17X
There is a 40.88% of reference with a coverageData >= 18X
There is a 38.59% of reference with a coverageData >= 19X
There is a 36.43% of reference with a coverageData >= 20X
There is a 34.32% of reference with a coverageData >= 21X
There is a 32.34% of reference with a coverageData >= 22X
There is a 30.42% of reference with a coverageData >= 23X
There is a 28.61% of reference with a coverageData >= 24X
There is a 26.87% of reference with a coverageData >= 25X
There is a 25.23% of reference with a coverageData >= 26X
There is a 23.66% of reference with a coverageData >= 27X
There is a 22.19% of reference with a coverageData >= 28X
There is a 20.79% of reference with a coverageData >= 29X
There is a 19.47% of reference with a coverageData >= 30X
There is a 18.22% of reference with a coverageData >= 31X
There is a 17.04% of reference with a coverageData >= 32X
There is a 15.93% of reference with a coverageData >= 33X
There is a 14.89% of reference with a coverageData >= 34X
There is a 13.91% of reference with a coverageData >= 35X
There is a 12.99% of reference with a coverageData >= 36X
There is a 12.12% of reference with a coverageData >= 37X
There is a 11.31% of reference with a coverageData >= 38X
There is a 10.55% of reference with a coverageData >= 39X
There is a 9.85% of reference with a coverageData >= 40X
There is a 9.18% of reference with a coverageData >= 41X
There is a 8.56% of reference with a coverageData >= 42X
There is a 7.98% of reference with a coverageData >= 43X
There is a 7.44% of reference with a coverageData >= 44X
There is a 6.93% of reference with a coverageData >= 45X
There is a 6.46% of reference with a coverageData >= 46X
There is a 6.02% of reference with a coverageData >= 47X
There is a 5.61% of reference with a coverageData >= 48X
There is a 5.23% of reference with a coverageData >= 49X
There is a 4.88% of reference with a coverageData >= 50X
There is a 4.54% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 4923624934 19.75371180318945 609.7859772296181
chr2 243199373 4906365792 20.17425345911562 129.82468297601025
chr3 198022430 3975536967 20.076195242124843 35.85930023472728
chr4 191154276 3898781591 20.39599465198466 116.86842805899244
chr5 180915260 3245790348 17.94094289226901 20.602871644537334
chr6 171115067 3607553149 21.082615413404827 86.2398527961044
chr7 159138663 3034808803 19.07021678949257 150.65866721228664
chr8 146364022 2573331835 17.58172397722167 85.30734542193672
chr9 141213431 2320287457 16.431067785613113 183.83388380891685
chr10 135534747 2866283667 21.147961909723417 448.71319068382
chr11 135006516 2523686414 18.693071184801184 135.76263448152605
chr12 133851895 2452810166 18.32480717587151 38.273852245708234
chr13 115169878 2025009686 17.582806556415733 17.824842681107658
chr14 107349540 1715180206 15.977527300070406 21.995829554990603
chr15 102531392 1659224754 16.182602436529876 23.29637690154192
chr16 90354753 1438391286 15.919375995637994 66.62660490283777
chr17 81195210 1871578854 23.050360409191626 119.92069733840358
chr18 78077248 1694218245 21.699256677182063 217.27000865750074
chr19 59128983 1112409905 18.813276477290334 305.0370685773127
chr20 63025520 1307634103 20.747692410947185 37.38394380883805
chr21 48129895 941377215 19.559095547580146 82.96579935633866
chr22 51304566 726133449 14.153388394319522 78.39476147686923
chrMT 16571 184873012 11156.418562549032 1969.442599855477
chrX 155270560 1630173574 10.498922487302165 53.98915853150434
chrY 59373566 665930186 11.215937173118421 264.18841314446087