BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1781879.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 = 222,247,104
number of mapped reads = 213,630,441 (96.12%)
number of supplementary alignments = 1,227,661 (0.55%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 107,530,749
number of mapped paired reads (second in pair) = 106,099,692
number of mapped paired reads (both in pair) = 210,934,626
number of mapped paired reads (singletons) = 2,695,815
number of mapped bases = 21,179,612,321 bp
number of sequenced bases = 21,175,482,244 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 25,472,570
duplication rate = 11.24%
>>>>>>> Insert size
mean insert size = 37,478.9789
std insert size = 1,874,821.5539
median insert size = 190
>>>>>>> Mapping quality
mean mapping quality = 53.8248
>>>>>>> ACTG content
number of A's = 6,179,219,969 bp (29.18%)
number of C's = 4,397,487,594 bp (20.77%)
number of T's = 6,135,905,733 bp (28.98%)
number of G's = 4,462,224,438 bp (21.07%)
number of N's = 644,510 bp (0%)
GC percentage = 41.84%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 99,774,805
number of insertions = 2,067,422
mapped reads with insertion percentage = 0.95%
number of deletions = 1,813,571
mapped reads with deletion percentage = 0.83%
homopolymer indels = 46.17%
>>>>>>> Coverage
mean coverageData = 6.8416X
std coverageData = 11.4301X
There is a 77.79% of reference with a coverageData >= 1X
There is a 66.73% of reference with a coverageData >= 2X
There is a 56.98% of reference with a coverageData >= 3X
There is a 48.95% of reference with a coverageData >= 4X
There is a 42.33% of reference with a coverageData >= 5X
There is a 36.85% of reference with a coverageData >= 6X
There is a 32.28% of reference with a coverageData >= 7X
There is a 28.44% of reference with a coverageData >= 8X
There is a 25.19% of reference with a coverageData >= 9X
There is a 22.41% of reference with a coverageData >= 10X
There is a 20.02% of reference with a coverageData >= 11X
There is a 17.95% of reference with a coverageData >= 12X
There is a 16.14% of reference with a coverageData >= 13X
There is a 14.56% of reference with a coverageData >= 14X
There is a 13.17% of reference with a coverageData >= 15X
There is a 11.94% of reference with a coverageData >= 16X
There is a 10.85% of reference with a coverageData >= 17X
There is a 9.88% of reference with a coverageData >= 18X
There is a 9.02% of reference with a coverageData >= 19X
There is a 8.25% of reference with a coverageData >= 20X
There is a 7.56% of reference with a coverageData >= 21X
There is a 6.93% of reference with a coverageData >= 22X
There is a 6.37% of reference with a coverageData >= 23X
There is a 5.86% of reference with a coverageData >= 24X
There is a 5.41% of reference with a coverageData >= 25X
There is a 4.99% of reference with a coverageData >= 26X
There is a 4.61% of reference with a coverageData >= 27X
There is a 4.27% of reference with a coverageData >= 28X
There is a 3.96% of reference with a coverageData >= 29X
There is a 3.67% of reference with a coverageData >= 30X
There is a 3.41% of reference with a coverageData >= 31X
There is a 3.17% of reference with a coverageData >= 32X
There is a 2.96% of reference with a coverageData >= 33X
There is a 2.75% of reference with a coverageData >= 34X
There is a 2.57% of reference with a coverageData >= 35X
There is a 2.4% of reference with a coverageData >= 36X
There is a 2.24% of reference with a coverageData >= 37X
There is a 2.1% of reference with a coverageData >= 38X
There is a 1.96% of reference with a coverageData >= 39X
There is a 1.84% of reference with a coverageData >= 40X
There is a 1.73% of reference with a coverageData >= 41X
There is a 1.62% of reference with a coverageData >= 42X
There is a 1.52% of reference with a coverageData >= 43X
There is a 1.43% of reference with a coverageData >= 44X
There is a 1.35% of reference with a coverageData >= 45X
There is a 1.27% of reference with a coverageData >= 46X
There is a 1.19% of reference with a coverageData >= 47X
There is a 1.13% of reference with a coverageData >= 48X
There is a 1.06% of reference with a coverageData >= 49X
There is a 1% of reference with a coverageData >= 50X
There is a 0.95% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 1570892112 6.302460173208555 13.413173690470758
chr2 243199373 1695585496 6.97199781020817 11.040912980943975
chr3 198022430 1354415528 6.839707643220013 9.993660029481635
chr4 191154276 1816353566 9.502029481150608 13.085370941395233
chr5 180915260 1099383183 6.076785247413623 9.015670287863019
chr6 171115067 1100205154 6.429621735180105 9.913316361847036
chr7 159138663 1026230892 6.4486585010457205 10.039281947535356
chr8 146364022 933648166 6.378945817709218 9.274672049137656
chr9 141213431 784966232 5.558722186985174 10.300364408833994
chr10 135534747 1410781500 10.409002349781197 16.281824387429584
chr11 135006516 939470580 6.958705459816473 10.52030959239518
chr12 133851895 1297117755 9.690693994283757 13.229681696293413
chr13 115169878 642060778 5.574901954832321 8.866953143940705
chr14 107349540 554735248 5.167560550329326 8.866206971032465
chr15 102531392 542676462 5.292783521362901 9.159628814637479
chr16 90354753 486245807 5.381518856014138 9.123444864862186
chr17 81195210 470206217 5.791058573529153 10.189577193933781
chr18 78077248 472095593 6.0465193778346285 11.036180506382333
chr19 59128983 239859297 4.056543590475757 9.655680121378717
chr20 63025520 395583301 6.276557511941195 10.042220879788292
chr21 48129895 220992798 4.59159110984971 11.962916061941549
chr22 51304566 196893883 3.8377458060945298 7.7977215894731895
chrMT 16571 960124 57.94001569006095 17.060324161182628
chrX 155270560 1904644134 12.26661470146047 15.972056470253335
chrY 59373566 23608515 0.3976266980494316 4.0596949407388525