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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,189,312 |
A→G |
T512A (ACC→GCC) |
metG → |
methionine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,189,312 | 0 | A | G | 93.9%
| 92.8
/ ‑2.2
| 33 | T512A (ACC→GCC) | metG | methionine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base A (0/2); new base G (10/21); total (10/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.03e-01 |
ACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAG > NZ_CP009273/2189226‑2189395
|
aCCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGTATTCCTCAATACGGAACTGACCt < 1:158785/90‑1 (MQ=255)
aCCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCt < 1:4215/90‑1 (MQ=255)
aCCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCt < 2:525993/90‑1 (MQ=255)
gTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGa > 2:532213/1‑90 (MQ=255)
ttCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGAt < 1:746020/90‑1 (MQ=255)
cgcgTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGt < 1:696167/90‑1 (MQ=255)
gcgTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTa > 2:167050/1‑90 (MQ=255)
gcgTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTa > 1:257282/1‑90 (MQ=255)
cTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAg > 1:467658/1‑90 (MQ=255)
tACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCgctg > 1:694888/1‑90 (MQ=255)
cTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGctgctg < 2:403103/90‑1 (MQ=255)
ccGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCcac < 2:694888/90‑1 (MQ=255)
ccGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCcac < 2:400262/90‑1 (MQ=255)
gTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACaaa > 2:526128/1‑90 (MQ=255)
gACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCaa < 1:234865/90‑1 (MQ=255)
cGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGgc < 2:257282/90‑1 (MQ=255)
aGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGgcgc < 1:17962/90‑1 (MQ=255)
aGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGgcgc < 2:465348/90‑1 (MQ=255)
aGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGgcgc < 2:465327/90‑1 (MQ=255)
aGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGgcgc < 1:808338/90‑1 (MQ=255)
aGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGgcgc < 1:49534/90‑1 (MQ=255)
cAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGtata < 2:265103/90‑1 (MQ=255)
gAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAAc < 1:442867/90‑1 (MQ=255)
gAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAAc < 1:205219/90‑1 (MQ=255)
ttCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATc < 2:628730/90‑1 (MQ=255)
aTACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCATAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATc > 2:438138/1‑83 (MQ=255)
aTACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCATAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATc < 1:438138/83‑1 (MQ=255)
aTACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGa > 2:28816/1‑90 (MQ=255)
cGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGc < 1:221425/90‑1 (MQ=255)
cGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGc < 2:574600/90‑1 (MQ=255)
ggAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCa < 1:694624/90‑1 (MQ=255)
gAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAg > 2:641395/1‑90 (MQ=255)
gAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAg > 2:75542/1‑90 (MQ=255)
|
ACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAG > NZ_CP009273/2189226‑2189395
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
CAATGGGCATCAACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGAAGCA > NZ_CP009273/2189214‑2189404
|
CAATGGGCATCAACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGC < SRR3722079.264812/100‑1 (MQ=60)
AGCCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTA > SRR3722079.259443/1‑100 (MQ=60)
ACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGTATTCCTCAATACGGAACTGACCTGGGATGGTAT < SRR3722079.160167/100‑1 (MQ=60)
ACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTAT < SRR3722079.4253/100‑1 (MQ=60)
GTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAG > SRR3722079.471747/1‑100 (MQ=60)
TTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGC < SRR3722079.753991/100‑1 (MQ=60)
CGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAAC < SRR3722079.703498/100‑1 (MQ=60)
GCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTG > SRR3722079.702203/1‑100 (MQ=60)
GACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTAT < SRR3722079.236850/100‑1 (MQ=60)
AGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCG < SRR3722079.18086/100‑1 (MQ=60)
AGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCG < SRR3722079.817005/100‑1 (MQ=60)
AGCGTGCAGAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCG < SRR3722079.49916/100‑1 (MQ=60)
GAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATA < SRR3722079.446732/100‑1 (MQ=60)
GAAGCATTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATA < SRR3722079.206988/100‑1 (MQ=60)
TTCCTCAATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCATAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGC < SRR3722079.441938/100‑1 (MQ=60)
ATACGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGA > SRR3722079.671307/1‑100 (MQ=60)
CGGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGAAGC < SRR3722079.223312/100‑1 (MQ=60)
GGAACTGGCCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGAAGCA < SRR3722079.701936/100‑1 (MQ=60)
|
CAATGGGCATCAACCTGTTCCGCGTGCTGATGACTTACCTGAAGCCGGTACTGCCGAAACTGACCGAGCGTGCAGAAGCATTCCTCAATACGGAACTGACCTGGGATGGTATCCAGCAACCGCTGCTGGGCCACAAAGTGAATCCGTTCAAGGCGCTGTATAACCGCATCGATATGAGGCAGGTTGAAGCA > NZ_CP009273/2189214‑2189404
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
