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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,076,727 |
(T)5→4 |
intergenic (+458/‑85) |
putP → / → BW25113_RS05295 |
sodium/proline symporter PutP/FTR1 family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,076,723 | 0 | T | . | 100.0%
| 58.2
/ NA
| 15 | intergenic (+454/‑89) | putP/BW25113_RS05295 | sodium/proline symporter PutP/FTR1 family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (13/2); total (13/2) |
CTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAG > NZ_CP009273/1076643‑1076801
|
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc > 1:164645/1‑90 (MQ=255)
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc > 2:135108/1‑90 (MQ=255)
aatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATg > 2:415721/1‑90 (MQ=255)
tttATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAAt > 2:382509/1‑90 (MQ=255)
cTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCAc > 1:142334/1‑90 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 2:219391/1‑90 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 2:352636/1‑90 (MQ=255)
ttGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCtt > 2:390968/1‑90 (MQ=255)
ttGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCtt > 2:83573/1‑90 (MQ=255)
tACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCAt < 1:370945/90‑1 (MQ=255)
cagcatcatTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGa > 1:173877/4‑90 (MQ=255)
tcatTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc < 1:54511/35‑1 (MQ=38)
tcatTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc > 2:54511/1‑35 (MQ=38)
atTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGGTAATCGCTATCACTGAGATTTACTTTTGTTTGCATAGATTGTCTCAGaa > 1:71747/1‑90 (MQ=255)
aTTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAg > 1:198570/1‑90 (MQ=255)
|
CTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAG > NZ_CP009273/1076643‑1076801
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCCCATCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAG > NZ_CP009273/1076628‑1076801
|
tataagagacagACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTC < SRR3722109.16656/88‑1 (MQ=60)
TCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGC > SRR3722109.166684/1‑100 (MQ=60)
acacattgacattcgtcggcagcgtcagatgtgtataagagacagCATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATA < SRR3722109.55162/55‑1 (MQ=60)
GTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCAC > SRR3722109.144099/1‑100 (MQ=60)
GTTTACATTCCAGCATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGA > SRR3722109.176024/1‑100 (MQ=60)
TACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTC < SRR3722109.376163/100‑1 (MQ=60)
TTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGGTAATCGCTATCACTGAGATTTACTTTTGTTTGCATAGATTGTCTCAGAA > SRR3722109.72617/1‑100 (MQ=60)
TTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAG > SRR3722109.200986/1‑100 (MQ=60)
|
TCCCATCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAG > NZ_CP009273/1076628‑1076801
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
