BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6008710.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,459,509
number of mapped reads = 1,044,378 (71.56%)
number of supplementary alignments = 4,159 (0.28%)
number of secondary alignments = 0
number of mapped bases = 70,540,024 bp
number of sequenced bases = 70,504,951 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 28,672
duplication rate = 2.12%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 48.7754
>>>>>>> ACTG content
number of A's = 21,881,045 bp (31.03%)
number of C's = 11,897,538 bp (16.87%)
number of T's = 21,024,839 bp (29.82%)
number of G's = 15,698,230 bp (22.27%)
number of N's = 3,299 bp (0%)
GC percentage = 39.14%
>>>>>>> Mismatches and indels
general error rate = 0.0095
number of mismatches = 658,183
number of insertions = 5,344
mapped reads with insertion percentage = 0.51%
number of deletions = 22,622
mapped reads with deletion percentage = 2.14%
homopolymer indels = 49.21%
>>>>>>> Coverage
mean coverageData = 0.0228X
std coverageData = 0.1937X
There is a 2.05% of reference with a coverageData >= 1X
There is a 0.16% of reference with a coverageData >= 2X
There is a 0.03% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% 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 6578973 0.026395011469199106 0.2250063413075814
chr2 243199373 6372450 0.026202575777199887 0.2887257742752714
chr3 198022430 5518579 0.027868454093811494 0.19007005949278322
chr4 191154276 3496740 0.01829276369417967 0.15198919388212456
chr5 180915260 3718269 0.020552544876535014 0.16003821773554383
chr6 171115067 3968297 0.02319080995947598 0.17632098430905604
chr7 159138663 2928311 0.01840100290398946 0.19326984313596995
chr8 146364022 4921903 0.03362782009365662 0.25106020845319654
chr9 141213431 2653357 0.018789692886932264 0.16910372178570554
chr10 135534747 3844987 0.028369013002990297 0.19608940322220317
chr11 135006516 3224206 0.023881854709886744 0.18473049031428307
chr12 133851895 3602600 0.026914822535758647 0.18432257252427878
chr13 115169878 2349689 0.020401940514341778 0.16330892910555617
chr14 107349540 2740769 0.02553125984517493 0.18292627284495694
chr15 102531392 1893665 0.018469124070801653 0.15277431121012464
chr16 90354753 1795675 0.01987360864126318 0.16194532860531732
chr17 81195210 1659038 0.02043270779150642 0.16512908750583372
chr18 78077248 1288962 0.016508804203754723 0.2225014731602723
chr19 59128983 931432 0.015752545583271743 0.16066249230821195
chr20 63025520 1279110 0.020295112202168265 0.15725083364054276
chr21 48129895 652491 0.01355687561753459 0.13268530823801167
chr22 51304566 823534 0.0160518656370663 0.13980947554456172
chrMT 16571 22943 1.3845271860479151 1.6595184665277476
chrX 155270560 4145561 0.026698950528677167 0.18502465105873683
chrY 59373566 128483 0.002163976473974967 0.05489399981131677