BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR5038416.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 13,850,194
number of mapped reads = 13,538,528 (97.75%)
number of supplementary alignments = 223,561 (1.61%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,833,217
number of mapped paired reads (second in pair) = 6,705,311
number of mapped paired reads (both in pair) = 13,397,220
number of mapped paired reads (singletons) = 141,308
number of mapped bases = 1,933,490,544 bp
number of sequenced bases = 1,932,241,216 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,761,577
duplication rate = 8.49%
>>>>>>> Insert size
mean insert size = 89,451.1221
std insert size = 2,880,299.6547
median insert size = 258
>>>>>>> Mapping quality
mean mapping quality = 53.7054
>>>>>>> ACTG content
number of A's = 555,580,742 bp (28.75%)
number of C's = 401,045,951 bp (20.76%)
number of T's = 555,875,684 bp (28.77%)
number of G's = 419,698,228 bp (21.72%)
number of N's = 40,611 bp (0%)
GC percentage = 42.48%
>>>>>>> Mismatches and indels
general error rate = 0.0135
number of mismatches = 25,318,945
number of insertions = 305,861
mapped reads with insertion percentage = 2.15%
number of deletions = 632,736
mapped reads with deletion percentage = 4.51%
homopolymer indels = 47.75%
>>>>>>> Coverage
mean coverageData = 0.6246X
std coverageData = 8.5431X
There is a 28.09% of reference with a coverageData >= 1X
There is a 14.29% of reference with a coverageData >= 2X
There is a 7.07% of reference with a coverageData >= 3X
There is a 3.92% of reference with a coverageData >= 4X
There is a 2.14% of reference with a coverageData >= 5X
There is a 1.24% of reference with a coverageData >= 6X
There is a 0.72% of reference with a coverageData >= 7X
There is a 0.44% of reference with a coverageData >= 8X
There is a 0.27% of reference with a coverageData >= 9X
There is a 0.18% of reference with a coverageData >= 10X
There is a 0.12% of reference with a coverageData >= 11X
There is a 0.09% of reference with a coverageData >= 12X
There is a 0.06% of reference with a coverageData >= 13X
There is a 0.05% of reference with a coverageData >= 14X
There is a 0.04% of reference with a coverageData >= 15X
There is a 0.03% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.02% of reference with a coverageData >= 22X
There is a 0.02% of reference with a coverageData >= 23X
There is a 0.02% of reference with a coverageData >= 24X
There is a 0.02% of reference with a coverageData >= 25X
There is a 0.02% of reference with a coverageData >= 26X
There is a 0.02% of reference with a coverageData >= 27X
There is a 0.02% of reference with a coverageData >= 28X
There is a 0.02% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 131024304 0.5256729290154908 14.082752472026453
chr2 243199373 220087150 0.904965943312691 10.983744675910902
chr3 198022430 128825748 0.6505613934744665 1.3153215862188068
chr4 191154276 85035380 0.4448520942319909 5.342977383725931
chr5 180915260 98670763 0.5453976795545052 1.2776594165794004
chr6 171115067 140400645 0.8205042809000566 13.202360085721256
chr7 159138663 133524616 0.8390457320858602 7.686891399796339
chr8 146364022 108101951 0.738582812379944 2.7678192462656512
chr9 141213431 82217921 0.5822245123411809 14.995305165392693
chr10 135534747 79912281 0.58960733515812 13.326426267674943
chr11 135006516 89043304 0.6595481954367299 7.6391863067625465
chr12 133851895 71157397 0.5316129218790664 1.2242367139795556
chr13 115169878 117847892 1.0232527293291047 1.9176346534207138
chr14 107349540 36595253 0.3408980886177994 1.1009514537330207
chr15 102531392 36789051 0.35880768106610705 0.9172197855191391
chr16 90354753 75008122 0.8301513701221672 8.84197715503163
chr17 81195210 51350069 0.6324273192962984 9.455248178375927
chr18 78077248 30936887 0.39623434217353565 13.032690105703786
chr19 59128983 30717305 0.5194965893460404 8.190113505643165
chr20 63025520 67737951 1.0747702041966491 2.4125539786349424
chr21 48129895 15754429 0.3273314641554901 2.327246951476687
chr22 51304566 14230881 0.27738039924165814 0.836302434958334
chrMT 16571 2014267 121.55373845875324 84.11330274166853
chrX 155270560 68650802 0.4421366291201629 2.037930881249327
chrY 59373566 17856175 0.3007428423618686 6.913066265979987