BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524458.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 521,628
number of mapped reads = 480,992 (92.21%)
number of supplementary alignments = 1,087 (0.21%)
number of secondary alignments = 0
number of mapped bases = 28,015,817 bp
number of sequenced bases = 28,006,519 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,481
duplication rate = 1.7%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.5201
>>>>>>> ACTG content
number of A's = 7,171,857 bp (25.61%)
number of C's = 5,177,529 bp (18.49%)
number of T's = 9,018,055 bp (32.2%)
number of G's = 6,638,494 bp (23.7%)
number of N's = 584 bp (0%)
GC percentage = 42.19%
>>>>>>> Mismatches and indels
general error rate = 0.0048
number of mismatches = 130,662
number of insertions = 1,997
mapped reads with insertion percentage = 0.41%
number of deletions = 5,325
mapped reads with deletion percentage = 1.1%
homopolymer indels = 40.51%
>>>>>>> Coverage
mean coverageData = 0.009X
std coverageData = 0.1161X
There is a 0.86% of reference with a coverageData >= 1X
There is a 0.04% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% 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 2760436 0.011074941313787138 0.17262284789673576
chr2 243199373 2209478 0.009085048093442247 0.12481907601463672
chr3 198022430 1548521 0.007819927267835265 0.09202375027467607
chr4 191154276 1589878 0.00831725051235579 0.09909630272523036
chr5 180915260 1540416 0.00851457196037526 0.09570550443594278
chr6 171115067 1238018 0.007235002865060386 0.09757158317555494
chr7 159138663 1393579 0.008757010859139868 0.13786064292659259
chr8 146364022 2567452 0.01754155129735366 0.14767591078893602
chr9 141213431 1162719 0.008233770624835254 0.10609117054502039
chr10 135534747 1473830 0.010874185643331744 0.1235537577980987
chr11 135006516 968454 0.007173387097849411 0.11000838105647177
chr12 133851895 1314994 0.009824246418027925 0.1030151074869918
chr13 115169878 621418 0.005395664307293961 0.07621890297244663
chr14 107349540 666165 0.006205569208773507 0.08249407901783438
chr15 102531392 734653 0.0071651519175707674 0.0893795126375086
chr16 90354753 850151 0.009409034630419498 0.10328145263860955
chr17 81195210 977111 0.012034096592643827 0.11685962072539077
chr18 78077248 664955 0.008516629582026251 0.15245772544538394
chr19 59128983 556755 0.009415940740939177 0.1291437665867419
chr20 63025520 793397 0.012588503831463826 0.11741435420445841
chr21 48129895 378289 0.007859751200371412 0.09340029466638562
chr22 51304566 221848 0.004324137543625259 0.06797907952130383
chrMT 16571 4410 0.26612757226479994 0.5306590456869934
chrX 155270560 1691867 0.010896251034323571 0.1123956335700805
chrY 59373566 87023 0.0014656859249451179 0.05124017025867513