BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524497.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 = 629,504
number of mapped reads = 581,506 (92.38%)
number of supplementary alignments = 1,322 (0.21%)
number of secondary alignments = 0
number of mapped bases = 33,894,449 bp
number of sequenced bases = 33,883,885 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 14,891
duplication rate = 2.04%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3946
>>>>>>> ACTG content
number of A's = 8,653,624 bp (25.54%)
number of C's = 6,596,544 bp (19.47%)
number of T's = 10,568,784 bp (31.19%)
number of G's = 8,064,263 bp (23.8%)
number of N's = 670 bp (0%)
GC percentage = 43.27%
>>>>>>> Mismatches and indels
general error rate = 0.0048
number of mismatches = 158,105
number of insertions = 1,830
mapped reads with insertion percentage = 0.31%
number of deletions = 6,097
mapped reads with deletion percentage = 1.04%
homopolymer indels = 44.54%
>>>>>>> Coverage
mean coverageData = 0.0109X
std coverageData = 0.1318X
There is a 1.02% of reference with a coverageData >= 1X
There is a 0.05% of reference with a coverageData >= 2X
There is a 0.01% 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 3350241 0.01344125437504928 0.20971992512009593
chr2 243199373 2653759 0.010911866125575908 0.1400841540748789
chr3 198022430 1859397 0.009389830232868065 0.10174814471804214
chr4 191154276 1896117 0.009919302040619797 0.11026116062663197
chr5 180915260 1856229 0.010260212433157933 0.10639197804159908
chr6 171115067 1476115 0.00862644667053194 0.1081567622123347
chr7 159138663 1669450 0.010490536796831075 0.15583648607713718
chr8 146364022 3096676 0.02115735791955758 0.16273617533565982
chr9 141213431 1439953 0.010196997479651918 0.11883286099940644
chr10 135534747 1780882 0.013139671113268098 0.13568127505233057
chr11 135006516 1186193 0.008786190734675355 0.12213883612519036
chr12 133851895 1573311 0.011754118236428406 0.11436223963054469
chr13 115169878 725203 0.006296811393687506 0.08338896381531292
chr14 107349540 813856 0.007581364577808158 0.09250861833256431
chr15 102531392 913387 0.008908364376833976 0.10009514842866113
chr16 90354753 1067052 0.011809583498059033 0.11589871493162077
chr17 81195210 1180607 0.014540352811452793 0.1298515629105451
chr18 78077248 792703 0.010152804053749435 0.16594812642329074
chr19 59128983 687706 0.011630607615896252 0.16000934900973826
chr20 63025520 979922 0.015548019278539868 0.1314532233374161
chr21 48129895 458753 0.009531560374274658 0.10627938571293544
chr22 51304566 273732 0.005335431548139399 0.07595939525704538
chrMT 16571 11682 0.7049665077545109 0.945136136161266
chrX 155270560 2046004 0.013177024672288165 0.12589773566719287
chrY 59373566 105519 0.0017772050275706869 0.05837786687433225