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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,771,044 |
A→G |
K96E (AAA→GAA) |
lldP → |
L‑lactate permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,771,044 | 0 | A | G | 100.0%
| 76.7
/ NA
| 23 | K96E (AAA→GAA) | lldP | L‑lactate permease |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/8); total (15/8) |
TGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTC > NZ_CP009273/3770964‑3771127
|
tggtTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGc < 2:169169/90‑1 (MQ=255)
tcttctACGGGTTGTGGCTCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGAcatca > 1:120611/1‑90 (MQ=255)
ggTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGt > 1:350721/1‑90 (MQ=255)
aTCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCg > 2:384518/1‑90 (MQ=255)
tCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGc > 2:368079/1‑74 (MQ=255)
tCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGc < 1:368079/74‑1 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGGAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 1:286919/90‑1 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 2:74877/90‑1 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 2:107405/90‑1 (MQ=255)
gcgTGGATCATTATTGCAGCGGTGTTCATCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 1:286921/90‑1 (MQ=255)
ttattGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGAcc > 1:233679/1‑90 (MQ=255)
gCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGt > 2:326866/1‑90 (MQ=255)
gCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGt > 1:274406/1‑90 (MQ=255)
aGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCt > 2:238928/1‑90 (MQ=255)
aGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCt > 2:264111/1‑90 (MQ=255)
ggTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa < 1:41139/70‑1 (MQ=255)
ggTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATa > 2:41139/1‑70 (MQ=255)
ataAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGAtcg > 1:76123/1‑90 (MQ=255)
ataAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGAtcg > 2:271076/1‑90 (MQ=255)
taAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGAtcgt < 2:203436/90‑1 (MQ=255)
ctcGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGttt > 2:431206/1‑90 (MQ=255)
tcGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTc > 2:142331/1‑90 (MQ=255)
tcGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTc > 2:426549/1‑90 (MQ=255)
|
TGGTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCGTCGGTTTC > NZ_CP009273/3770964‑3771127
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCG > NZ_CP009273/3770966‑3771119
|
GTTTATGGTTTCTTCTACGGGTTGTGGCTCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCA > SRR3722087.121756/1‑100 (MQ=60)
TTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGT > SRR3722087.354652/1‑100 (MQ=60)
agacaGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTC < SRR3722087.372268/95‑1 (MQ=60)
taagagacagTTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC < SRR3722087.41468/90‑1 (MQ=60)
GCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGGAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACT < SRR3722087.289812/100‑1 (MQ=60)
GCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC > SRR3722087.235838/1‑100 (MQ=60)
GCGTGGATCATTATTGCAGCGGTGTTCATCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACC < SRR3722087.289814/100‑1 (MQ=60)
GATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGT > SRR3722087.277115/1‑100 (MQ=60)
GTGTTCGTCTATAAGATCTCGGTGGAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCG > SRR3722087.76822/1‑100 (MQ=60)
|
GTTTATGGTTTCTTCTACGGGTTGTGGCCCATCGCGTGGATCATTATTGCAGCGGTGTTCGTCTATAAGATCTCGGTGAAAACCGGGCAGTTTGACATCATTCGCTCGTCTATTCTTTCGATAACCCCTGACCAGCGTCTGCAAATGCTGATCG > NZ_CP009273/3770966‑3771119
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
