BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1779222.sorted.bam
outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 10,170,782
number of mapped reads = 9,863,225 (96.98%)
number of supplementary alignments = 24,610 (0.24%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 4,968,515
number of mapped paired reads (second in pair) = 4,894,710
number of mapped paired reads (both in pair) = 9,775,410
number of mapped paired reads (singletons) = 87,815
number of mapped bases = 784,822,983 bp
number of sequenced bases = 784,674,212 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 157,429
duplication rate = 1.46%
>>>>>>> Insert size
mean insert size = 54,468.0711
std insert size = 2,217,101.5976
median insert size = 204
>>>>>>> Mapping quality
mean mapping quality = 53.1779
>>>>>>> ACTG content
number of A's = 239,242,961 bp (30.49%)
number of C's = 152,432,195 bp (19.43%)
number of T's = 236,855,196 bp (30.19%)
number of G's = 155,995,313 bp (19.88%)
number of N's = 148,547 bp (0.02%)
GC percentage = 39.31%
>>>>>>> Mismatches and indels
general error rate = 0.004
number of mismatches = 3,001,163
number of insertions = 56,400
mapped reads with insertion percentage = 0.57%
number of deletions = 71,884
mapped reads with deletion percentage = 0.72%
homopolymer indels = 46.7%
>>>>>>> Coverage
mean coverageData = 0.2535X
std coverageData = 0.8799X
There is a 15.38% of reference with a coverageData >= 1X
There is a 5.38% of reference with a coverageData >= 2X
There is a 2.15% of reference with a coverageData >= 3X
There is a 0.97% of reference with a coverageData >= 4X
There is a 0.48% of reference with a coverageData >= 5X
There is a 0.26% of reference with a coverageData >= 6X
There is a 0.15% of reference with a coverageData >= 7X
There is a 0.09% of reference with a coverageData >= 8X
There is a 0.06% of reference with a coverageData >= 9X
There is a 0.05% of reference with a coverageData >= 10X
There is a 0.04% of reference with a coverageData >= 11X
There is a 0.03% of reference with a coverageData >= 12X
There is a 0.03% of reference with a coverageData >= 13X
There is a 0.02% of reference with a coverageData >= 14X
There is a 0.02% of reference with a coverageData >= 15X
There is a 0.02% of reference with a coverageData >= 16X
There is a 0.02% 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 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% 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 57172961 0.2293794124589162 0.9065756207070734
chr2 243199373 55661064 0.22887009663466526 0.694363557209788
chr3 198022430 57887940 0.2923302173395206 0.7829027806684316
chr4 191154276 50466881 0.26401125863383773 0.7425900941070841
chr5 180915260 47076774 0.2602145004241212 0.7423635962034177
chr6 171115067 53332700 0.3116774047723103 0.8283866635612617
chr7 159138663 63166649 0.396928363033941 2.0143431304466826
chr8 146364022 63790401 0.4358338895606463 0.9992382231880438
chr9 141213431 40668414 0.2879925352143027 0.8319695911905179
chr10 135534747 17267788 0.12740487869136613 0.8766040765452411
chr11 135006516 30461736 0.22563159840373928 0.6967571049180833
chr12 133851895 35958824 0.268646357229384 0.7554328065139883
chr13 115169878 22340532 0.19397894994731174 0.6468728794742372
chr14 107349540 27028377 0.2517791599293299 0.7464464877387896
chr15 102531392 22093705 0.2154823471039972 0.6967674053809506
chr16 90354753 21923102 0.24263363323011905 0.723880479247154
chr17 81195210 16671225 0.20532276472959426 0.6548315411519254
chr18 78077248 14558527 0.18646311663034024 0.6327547910277177
chr19 59128983 11162521 0.18878256370484167 0.6901551925692111
chr20 63025520 14538125 0.2306704490498452 0.6937564398948679
chr21 48129895 8345905 0.1734037649573098 0.611626527056951
chr22 51304566 5644582 0.11002104569016333 0.4408702647637239
chrMT 16571 5504 0.3321465210307163 0.6475172522898295
chrX 155270560 47145322 0.30363336101834115 0.8731840131643988
chrY 59373566 453424 0.007636799177600348 0.10931457692223465