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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,065,206 |
A→T |
L269Q (CTG→CAG) |
yihT ← |
sulfofructosephosphate aldolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,065,206 | 0 | A | T | 95.0%
| 138.9
/ ‑0.4
| 40 | L269Q (CTG→CAG) | yihT | sulfofructosephosphate aldolase |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base T (16/22); total (17/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.08e-01 |
TATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCAGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGCGCCCGCCGTCATTGCC > NZ_CP009273/4065123‑4065292
|
tATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCa < 1:472663/90‑1 (MQ=255)
tCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCg > 2:645608/1‑90 (MQ=255)
tCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCg > 2:521367/1‑90 (MQ=255)
tCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCg > 1:627273/1‑90 (MQ=255)
cATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGt > 2:872397/1‑90 (MQ=255)
tCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTg < 2:384992/90‑1 (MQ=255)
tCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTg < 2:165007/90‑1 (MQ=255)
ttAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTc < 1:332364/90‑1 (MQ=255)
tAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCAGCATCAGCTCGTTGTCt > 1:429716/1‑90 (MQ=255)
tAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGCCACGCTGCATCAGCTCGTTGTCt > 2:919805/1‑90 (MQ=255)
ggcgTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTa < 1:958349/90‑1 (MQ=255)
gcgTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTaa > 1:221751/1‑90 (MQ=255)
gTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAAc > 1:325639/1‑90 (MQ=255)
gTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAAc > 2:266400/1‑90 (MQ=255)
gCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACcgacg < 1:182106/90‑1 (MQ=255)
gCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACcgacg < 2:1941/90‑1 (MQ=255)
tcatTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCg < 1:363514/90‑1 (MQ=255)
tcatTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCg < 1:603005/90‑1 (MQ=255)
tcatTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCg < 1:322829/90‑1 (MQ=255)
tcatTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCg < 1:737967/90‑1 (MQ=255)
tcatTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCg < 1:919805/90‑1 (MQ=255)
tcatTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCg < 2:811970/90‑1 (MQ=255)
tcatTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCg < 2:803928/90‑1 (MQ=255)
tcatTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCAGCATCAGCTCGTTGTCTGGTAAACCGACGACCg < 2:347719/90‑1 (MQ=255)
tcgACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAATGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAg < 1:620148/90‑1 (MQ=255)
tcgACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAg < 2:102339/90‑1 (MQ=255)
atCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACg < 2:540058/90‑1 (MQ=255)
tCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACgg > 1:131429/1‑90 (MQ=255)
gttgttGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCa > 2:713492/1‑90 (MQ=255)
tgttgtAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAgg < 1:122277/90‑1 (MQ=255)
cGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATgc > 2:59707/1‑90 (MQ=255)
ggTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATgcg < 2:5826/90‑1 (MQ=255)
tGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATgc < 2:310540/87‑1 (MQ=255)
tGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATgc > 1:310540/1‑87 (MQ=255)
tGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGcgcc > 2:422636/1‑90 (MQ=255)
tGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTAGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGcgcc > 2:604061/1‑90 (MQ=255)
gcgcAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGcgccc > 1:218395/1‑90 (MQ=255)
gcgcAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGcgccc < 2:394556/90‑1 (MQ=255)
gcAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGcgcccgc > 2:381889/1‑90 (MQ=255)
cGCTGCATCAGCTCGTTGTCTGGTAACCCGACGCCCGATGCCCAGACTGCCCGGCCTGCCAGGAATCCCGATGCGCCCGCCGTCATTGcc < 1:563076/90‑1 (MQ=255)
|
TATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCAGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGCGCCCGCCGTCATTGCC > NZ_CP009273/4065123‑4065292
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 31 ≤ 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
TTCATTCCTTTTATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCAGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGCGCCCGCCGTCATTGCCACGCGTACGG > NZ_CP009273/4065112‑4065302
|
TTCATTCCTTTTATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATC < SRR3722236.183886/100‑1 (MQ=60)
CCTTTTATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCG > SRR3722236.637448/1‑100 (MQ=60)
TATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTC < SRR3722236.479690/100‑1 (MQ=60)
ATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCAGCATCAGCTCGTTGTCT > SRR3722236.435721/1‑100 (MQ=60)
CATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAA > SRR3722236.225047/1‑100 (MQ=60)
TCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAAC > SRR3722236.330285/1‑100 (MQ=60)
TTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCG < SRR3722236.337109/100‑1 (MQ=60)
GGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGAC < SRR3722236.975258/100‑1 (MQ=60)
GCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCC < SRR3722236.184799/100‑1 (MQ=60)
TCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGAC < SRR3722236.327441/100‑1 (MQ=60)
TCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGAC < SRR3722236.368646/100‑1 (MQ=60)
TCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGAC < SRR3722236.612591/100‑1 (MQ=60)
TCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGAC < SRR3722236.750567/100‑1 (MQ=60)
TCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGAC < SRR3722236.936059/100‑1 (MQ=60)
acctaagccttcgtcggcagcgtcagatgtgtataagagacagCGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCAC < SRR3722236.278766/57‑1 (MQ=60)
GTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGG > SRR3722236.133309/1‑100 (MQ=60)
TCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAATGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGC < SRR3722236.630160/100‑1 (MQ=60)
TGTTGTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATG < SRR3722236.123998/100‑1 (MQ=60)
GTAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGCGCC > SRR3722236.315009/1‑100 (MQ=60)
TAATTTCGGTGCGCAAACGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGCGCCC > SRR3722236.221647/1‑100 (MQ=60)
CGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACctgtctcttatacacatctgacgctgccgacgaaggcttaggtgtaga > SRR3722236.848553/1‑52 (MQ=60)
CGTCACGCTGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGCGCCCGCCGTCATTGCCACGCG > SRR3722236.111371/1‑100 (MQ=60)
CGCTGCATCAGCTCGTTGTCTGGTAACCCGACGCCCGATGCCCAGACTGCCCGGCCTGCCAGGAATCCCGATGCGCCCGCCGTCATTGCCACGCGTACGG < SRR3722236.571740/100‑1 (MQ=60)
|
TTCATTCCTTTTATCCTCATCTTAGCGGCGTTTAGCCATCATTTCGTCGACGATATCGCCAAGTTGTTGTAATTTCGGTGCGCAAACGTCACGCAGCATCAGCTCGTTGTCTGGTAAACCGACGACCGATGCCCAGACTGCACGGCCTGCCAGGAATCCCGATGCGCCCGCCGTCATTGCCACGCGTACGG > NZ_CP009273/4065112‑4065302
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
