BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1781852.sorted.bam
outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 140,060,140
number of mapped reads = 136,046,123 (97.13%)
number of supplementary alignments = 394,386 (0.28%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 68,550,913
number of mapped paired reads (second in pair) = 67,495,210
number of mapped paired reads (both in pair) = 133,341,040
number of mapped paired reads (singletons) = 2,705,083
number of mapped bases = 13,504,743,474 bp
number of sequenced bases = 13,502,042,536 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 8,027,980
duplication rate = 5.67%
>>>>>>> Insert size
mean insert size = 43,687.7501
std insert size = 2,063,375.7596
median insert size = 203
>>>>>>> Mapping quality
mean mapping quality = 53.8762
>>>>>>> ACTG content
number of A's = 4,029,478,038 bp (29.84%)
number of C's = 2,727,839,863 bp (20.2%)
number of T's = 3,991,193,621 bp (29.56%)
number of G's = 2,749,446,553 bp (20.36%)
number of N's = 4,084,461 bp (0.03%)
GC percentage = 40.57%
>>>>>>> Mismatches and indels
general error rate = 0.0048
number of mismatches = 61,545,581
number of insertions = 1,601,807
mapped reads with insertion percentage = 1.16%
number of deletions = 1,191,830
mapped reads with deletion percentage = 0.86%
homopolymer indels = 47.41%
>>>>>>> Coverage
mean coverageData = 4.3624X
std coverageData = 5.6483X
There is a 80.96% of reference with a coverageData >= 1X
There is a 68.49% of reference with a coverageData >= 2X
There is a 56.06% of reference with a coverageData >= 3X
There is a 45.03% of reference with a coverageData >= 4X
There is a 35.8% of reference with a coverageData >= 5X
There is a 28.35% of reference with a coverageData >= 6X
There is a 22.44% of reference with a coverageData >= 7X
There is a 17.81% of reference with a coverageData >= 8X
There is a 14.19% of reference with a coverageData >= 9X
There is a 11.36% of reference with a coverageData >= 10X
There is a 9.14% of reference with a coverageData >= 11X
There is a 7.4% of reference with a coverageData >= 12X
There is a 6.02% of reference with a coverageData >= 13X
There is a 4.93% of reference with a coverageData >= 14X
There is a 4.06% of reference with a coverageData >= 15X
There is a 3.36% of reference with a coverageData >= 16X
There is a 2.79% of reference with a coverageData >= 17X
There is a 2.34% of reference with a coverageData >= 18X
There is a 1.96% of reference with a coverageData >= 19X
There is a 1.66% of reference with a coverageData >= 20X
There is a 1.4% of reference with a coverageData >= 21X
There is a 1.2% of reference with a coverageData >= 22X
There is a 1.02% of reference with a coverageData >= 23X
There is a 0.88% of reference with a coverageData >= 24X
There is a 0.75% of reference with a coverageData >= 25X
There is a 0.65% of reference with a coverageData >= 26X
There is a 0.56% of reference with a coverageData >= 27X
There is a 0.49% of reference with a coverageData >= 28X
There is a 0.43% of reference with a coverageData >= 29X
There is a 0.38% of reference with a coverageData >= 30X
There is a 0.33% of reference with a coverageData >= 31X
There is a 0.29% of reference with a coverageData >= 32X
There is a 0.26% of reference with a coverageData >= 33X
There is a 0.23% of reference with a coverageData >= 34X
There is a 0.2% of reference with a coverageData >= 35X
There is a 0.18% of reference with a coverageData >= 36X
There is a 0.16% of reference with a coverageData >= 37X
There is a 0.15% of reference with a coverageData >= 38X
There is a 0.13% of reference with a coverageData >= 39X
There is a 0.12% of reference with a coverageData >= 40X
There is a 0.11% of reference with a coverageData >= 41X
There is a 0.1% of reference with a coverageData >= 42X
There is a 0.09% of reference with a coverageData >= 43X
There is a 0.08% of reference with a coverageData >= 44X
There is a 0.08% of reference with a coverageData >= 45X
There is a 0.07% of reference with a coverageData >= 46X
There is a 0.06% of reference with a coverageData >= 47X
There is a 0.06% of reference with a coverageData >= 48X
There is a 0.05% of reference with a coverageData >= 49X
There is a 0.05% of reference with a coverageData >= 50X
There is a 0.05% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 1060354855 4.25417136673854 7.5775176233667505
chr2 243199373 1648699614 6.7792099694270185 7.117022467170156
chr3 198022430 480930387 2.4286662223062305 2.868635080945543
chr4 191154276 878905160 4.597883857957747 4.807037380984812
chr5 180915260 819343400 4.528879432282274 4.436707978176179
chr6 171115067 794004914 4.640181182876199 4.859805529820813
chr7 159138663 690830299 4.341058834960804 5.478990867003379
chr8 146364022 672481005 4.594578611675484 4.611578923091724
chr9 141213431 542110281 3.8389427773339775 5.616463671358661
chr10 135534747 726535028 5.360507501445367 8.288744805732604
chr11 135006516 617086105 4.570787568505212 4.812852960477388
chr12 133851895 885555867 6.615938212903149 6.499947662049276
chr13 115169878 413657630 3.5917171849396246 4.157950279067375
chr14 107349540 393545825 3.666022462695229 4.42221283752369
chr15 102531392 369065204 3.5995337310937905 4.497060406668865
chr16 90354753 297083182 3.287964076444324 4.2739322267930095
chr17 81195210 271848692 3.348087799760602 4.326154087108051
chr18 78077248 333772538 4.27490141558268 5.0042339996762495
chr19 59128983 175076628 2.960927435535294 5.101328746392557
chr20 63025520 243982751 3.871173946680646 5.319756089259915
chr21 48129895 155365109 3.2280375637636443 5.797431560790776
chr22 51304566 110639557 2.1565245674234923 3.4843081629418364
chrMT 16571 315097 19.014965904290626 6.891269292794384
chrX 155270560 911716386 5.871791703462653 6.0400052196873615
chrY 59373566 11837960 0.19938098378662317 2.1398979138657417