BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238030.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 = 2,555,465
number of mapped reads = 2,269,937 (88.83%)
number of supplementary alignments = 21,250 (0.83%)
number of secondary alignments = 0
number of mapped bases = 151,723,842 bp
number of sequenced bases = 151,643,492 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 126,660
duplication rate = 4.28%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7726
>>>>>>> ACTG content
number of A's = 41,783,437 bp (27.55%)
number of C's = 28,399,553 bp (18.73%)
number of T's = 47,765,656 bp (31.5%)
number of G's = 33,673,038 bp (22.21%)
number of N's = 21,808 bp (0.01%)
GC percentage = 40.93%
>>>>>>> Mismatches and indels
general error rate = 0.008
number of mismatches = 1,189,811
number of insertions = 11,090
mapped reads with insertion percentage = 0.48%
number of deletions = 44,730
mapped reads with deletion percentage = 1.95%
homopolymer indels = 45.08%
>>>>>>> Coverage
mean coverageData = 0.049X
std coverageData = 0.4453X
There is a 3.76% of reference with a coverageData >= 1X
There is a 0.78% of reference with a coverageData >= 2X
There is a 0.19% of reference with a coverageData >= 3X
There is a 0.05% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% 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 12365832 0.04961204088634949 0.7218333083494032
chr2 243199373 16159466 0.06644534400177092 0.5479032148175058
chr3 198022430 11250030 0.05681189752090205 0.2969714228055194
chr4 191154276 12318196 0.06444112189255971 0.3546952890460163
chr5 180915260 8882157 0.049095676064031306 0.27725967323235173
chr6 171115067 9665167 0.05648343637676278 0.3538507386613074
chr7 159138663 7970453 0.05008495641313764 0.5259434734999112
chr8 146364022 6897323 0.047124442918082696 0.6056767013078288
chr9 141213431 7052199 0.049940001811867314 0.4627594832475065
chr10 135534747 5215553 0.03848129808365673 0.4464580226616297
chr11 135006516 6178720 0.04576608731981499 0.3752900913177202
chr12 133851895 5115718 0.038219242245318974 0.2524068365393051
chr13 115169878 4304469 0.03737495493396285 0.23937631017883373
chr14 107349540 3855446 0.03591488142380489 0.2872173033270669
chr15 102531392 3119949 0.030429207476281996 0.21896038280608038
chr16 90354753 5059497 0.0559959142381807 0.3404449739036172
chr17 81195210 4548044 0.056013698345013206 0.3588446555978973
chr18 78077248 3799005 0.048657004406712695 0.834505991431169
chr19 59128983 1391189 0.023528038694661805 0.5748104967868956
chr20 63025520 2480052 0.03934996490310592 0.2638697542406033
chr21 48129895 2188989 0.04548085966113161 0.31253155527612153
chr22 51304566 1631031 0.03179114701019009 0.22172564062614572
chrMT 16571 14162 0.8546255506607929 1.1757188607835736
chrX 155270560 9828721 0.06330060894995163 0.370900718988655
chrY 59373566 432474 0.007283948550437412 0.21885271133852363