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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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%
| 50.3
/ NA
| 13 | 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 . (10/3); total (10/3) |
CTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAA > NZ_CP009273/1076643‑1076793
|
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc > 1:295220/1‑90 (MQ=255)
cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc > 2:301390/1‑90 (MQ=255)
aatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATg > 2:191214/1‑90 (MQ=255)
gTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATaa < 2:572186/90‑1 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 2:192859/1‑90 (MQ=255)
ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt > 2:338306/1‑90 (MQ=255)
tACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGAttt > 1:252697/1‑90 (MQ=255)
tttACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATaa > 1:497681/1‑60 (MQ=255)
tttACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATaa < 2:497681/60‑1 (MQ=255)
tcatTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAg > 1:18700/1‑90 (MQ=255)
tcatTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAg > 2:399874/1‑90 (MQ=255)
atTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGaa > 1:390437/1‑90 (MQ=255)
ttATAAGCATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGaaaaa < 1:74757/90‑1 (MQ=255)
|
CTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAA > NZ_CP009273/1076643‑1076793
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGTTCCGT > NZ_CP009273/1076633‑1076824
|
TCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGC > SRR3722111.299009/1‑100 (MQ=60)
CCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTT > SRR3722111.255670/1‑100 (MQ=60)
CCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACctgtctcttatacacatctg > SRR3722111.505338/1‑80 (MQ=60)
CATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAG > SRR3722111.18928/1‑100 (MQ=60)
TTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAA > SRR3722111.396088/1‑100 (MQ=60)
TTATAAGCATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGG < SRR3722111.75660/100‑1 (MQ=60)
TTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGTTCCGT < SRR3722111.76966/100‑1 (MQ=60)
|
TCTTTCTACCCTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAACGTTTAAGGGTGGGTGGCATGTTTGTTCCGT > NZ_CP009273/1076633‑1076824
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
