Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,575,877 |
(A)6→5 |
coding (655/1179 nt) |
hcp → |
Hcp1 family type VI secretion system effector |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,575,872 | 0 | A | . | 100.0%
| 83.6
/ NA
| 21 | coding (650/1179 nt) | hcp | Hcp1 family type VI secretion system effector |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (8/13); total (8/13) |
ATGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGAAAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGAAATA > NZ_CP009273/3575791‑3575951
|
aTGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGaaaaacagc > 2:26140/1‑86 (MQ=255)
gggAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGaaaaacag < 1:214013/87‑4 (MQ=255)
gggAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGaaaaacag > 2:214013/1‑84 (MQ=255)
aaCATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCa > 2:385653/1‑90 (MQ=255)
aTTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAg > 2:373698/1‑90 (MQ=255)
aTTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAg > 1:297562/1‑90 (MQ=255)
cAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACa > 2:14941/1‑90 (MQ=255)
cAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACa < 2:97714/90‑1 (MQ=255)
cAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACa < 1:357008/90‑1 (MQ=255)
aTACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAACACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATc > 2:367903/1‑90 (MQ=255)
aCTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTa < 1:385653/90‑1 (MQ=255)
ttGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTAt > 1:227989/2‑90 (MQ=255)
aaaaCTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTa > 1:195012/1‑90 (MQ=255)
cTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACaa < 2:195012/90‑1 (MQ=255)
tGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACaaa < 1:193309/90‑1 (MQ=255)
gggTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAg < 2:440874/90‑1 (MQ=255)
gagaTGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTc < 2:439838/90‑1 (MQ=255)
gaTGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTa < 1:366030/90‑1 (MQ=255)
tGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAAt < 1:199627/90‑1 (MQ=255)
aTAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTg < 1:167264/90‑1 (MQ=255)
aaaaGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGAt < 1:26140/90‑1 (MQ=255)
aGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACa < 1:112396/90‑1 (MQ=255)
aTGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATAc < 2:375722/90‑1 (MQ=255)
aaTACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGaaata > 2:207504/1‑90 (MQ=255)
|
ATGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGAAAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGAAATA > NZ_CP009273/3575791‑3575951
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAATGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGAAAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGAAA > NZ_CP009273/3575789‑3575949
|
CAATGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAG > SRR3722113.300365/1‑100 (MQ=60)
AATGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGC < SRR3722113.215686/100‑1 (MQ=60)
TTCAGAGATATTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTAT > SRR3722113.229889/1‑100 (MQ=60)
CAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTC < SRR3722113.360661/100‑1 (MQ=60)
ATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTA > SRR3722113.196531/1‑100 (MQ=60)
ACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAAC < SRR3722113.389684/100‑1 (MQ=60)
TGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAAT < SRR3722113.194814/100‑1 (MQ=60)
GATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATAC < SRR3722113.369808/100‑1 (MQ=60)
TGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACAT < SRR3722113.201171/100‑1 (MQ=60)
ATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATAC < SRR3722113.168619/100‑1 (MQ=60)
AAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAG < SRR3722113.26361/100‑1 (MQ=60)
AGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGAAA < SRR3722113.113379/100‑1 (MQ=60)
|
CAATGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGAAAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGAAA > NZ_CP009273/3575789‑3575949
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
