BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR504608.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 424,362,244
number of mapped reads = 283,163,794 (66.73%)
number of supplementary alignments = 1,793,426 (0.42%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 141,720,346
number of mapped paired reads (second in pair) = 141,443,448
number of mapped paired reads (both in pair) = 281,438,970
number of mapped paired reads (singletons) = 1,724,824
number of mapped bases = 28,122,105,699 bp
number of sequenced bases = 28,114,941,258 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 72,025,806
duplication rate = 22.17%
>>>>>>> Insert size
mean insert size = 24,246.3897
std insert size = 1,501,934.0719
median insert size = 207
>>>>>>> Mapping quality
mean mapping quality = 53.7767
>>>>>>> ACTG content
number of A's = 7,260,767,699 bp (25.83%)
number of C's = 6,735,146,360 bp (23.96%)
number of T's = 7,309,151,490 bp (26%)
number of G's = 6,804,147,423 bp (24.2%)
number of N's = 5,728,286 bp (0.02%)
GC percentage = 48.16%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 139,205,069
number of insertions = 2,096,186
mapped reads with insertion percentage = 0.72%
number of deletions = 2,767,158
mapped reads with deletion percentage = 0.95%
homopolymer indels = 39.93%
>>>>>>> Coverage
mean coverageData = 9.0843X
std coverageData = 23.3378X
There is a 67.73% of reference with a coverageData >= 1X
There is a 57.71% of reference with a coverageData >= 2X
There is a 50.13% of reference with a coverageData >= 3X
There is a 44.3% of reference with a coverageData >= 4X
There is a 39.51% of reference with a coverageData >= 5X
There is a 35.53% of reference with a coverageData >= 6X
There is a 32.15% of reference with a coverageData >= 7X
There is a 29.25% of reference with a coverageData >= 8X
There is a 26.73% of reference with a coverageData >= 9X
There is a 24.53% of reference with a coverageData >= 10X
There is a 22.6% of reference with a coverageData >= 11X
There is a 20.88% of reference with a coverageData >= 12X
There is a 19.35% of reference with a coverageData >= 13X
There is a 17.99% of reference with a coverageData >= 14X
There is a 16.76% of reference with a coverageData >= 15X
There is a 15.65% of reference with a coverageData >= 16X
There is a 14.65% of reference with a coverageData >= 17X
There is a 13.73% of reference with a coverageData >= 18X
There is a 12.9% of reference with a coverageData >= 19X
There is a 12.14% of reference with a coverageData >= 20X
There is a 11.45% of reference with a coverageData >= 21X
There is a 10.81% of reference with a coverageData >= 22X
There is a 10.22% of reference with a coverageData >= 23X
There is a 9.68% of reference with a coverageData >= 24X
There is a 9.17% of reference with a coverageData >= 25X
There is a 8.71% of reference with a coverageData >= 26X
There is a 8.27% of reference with a coverageData >= 27X
There is a 7.87% of reference with a coverageData >= 28X
There is a 7.5% of reference with a coverageData >= 29X
There is a 7.15% of reference with a coverageData >= 30X
There is a 6.82% of reference with a coverageData >= 31X
There is a 6.51% of reference with a coverageData >= 32X
There is a 6.23% of reference with a coverageData >= 33X
There is a 5.96% of reference with a coverageData >= 34X
There is a 5.71% of reference with a coverageData >= 35X
There is a 5.47% of reference with a coverageData >= 36X
There is a 5.25% of reference with a coverageData >= 37X
There is a 5.04% of reference with a coverageData >= 38X
There is a 4.84% of reference with a coverageData >= 39X
There is a 4.65% of reference with a coverageData >= 40X
There is a 4.47% of reference with a coverageData >= 41X
There is a 4.3% of reference with a coverageData >= 42X
There is a 4.15% of reference with a coverageData >= 43X
There is a 3.99% of reference with a coverageData >= 44X
There is a 3.85% of reference with a coverageData >= 45X
There is a 3.72% of reference with a coverageData >= 46X
There is a 3.59% of reference with a coverageData >= 47X
There is a 3.46% of reference with a coverageData >= 48X
There is a 3.35% of reference with a coverageData >= 49X
There is a 3.23% of reference with a coverageData >= 50X
There is a 3.13% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 2849695616 11.433053223967695 22.780163401037314
chr2 243199373 1255333196 5.16174519907171 12.909995060264468
chr3 198022430 1588475520 8.021694916075921 21.70288227877772
chr4 191154276 949940104 4.9694943993824126 9.446168958500719
chr5 180915260 1371219673 7.579347773095536 21.63491790077764
chr6 171115067 1192573473 6.969424106878911 13.534632174681233
chr7 159138663 2249662323 14.136491287475502 26.07353038399645
chr8 146364022 2535728840 17.324809781463916 41.396222257429606
chr9 141213431 858691203 6.080804049014289 16.997844627276205
chr10 135534747 1382079463 10.19723350352364 21.089530971497794
chr11 135006516 1583926089 11.732219569313232 26.94576292698955
chr12 133851895 847757560 6.3335491813545115 15.605077523890298
chr13 115169878 769601285 6.682313972755967 14.88657742712101
chr14 107349540 997047713 9.28786199735928 18.557963701159537
chr15 102531392 857581099 8.36408325559454 17.40268670637873
chr16 90354753 1049905842 11.619818627582326 26.210860729633225
chr17 81195210 1364377891 16.8036746379497 54.082009931582945
chr18 78077248 643250406 8.238640865005898 23.60726873081342
chr19 59128983 590782898 9.991426674800072 21.420885892119085
chr20 63025520 1595097069 25.308749043244706 45.18634909546438
chr21 48129895 234497899 4.872188044457608 12.588501524015841
chr22 51304566 308867361 6.020270418036477 15.559900234413805
chrMT 16571 483272 29.16371975137288 13.528971985134092
chrX 155270560 1018499072 6.559511809579356 12.259485810284758
chrY 59373566 27030832 0.4552671133143662 10.547395615783142