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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,003,480 |
T→C |
F60S (TTC→TCC) |
yedK → |
SOS response‑associated peptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,003,480 | 0 | T | C | 97.0%
| 100.4
/ ‑3.4
| 33 | F60S (TTC→TCC) | yedK | SOS response‑associated peptidase |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (16/16); total (17/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.00e-01 |
ACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGT > NZ_CP009273/2003394‑2003556
|
aCCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTg < 1:1197743/90‑1 (MQ=255)
ccATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTggg < 1:707167/90‑1 (MQ=255)
aTTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGa > 1:466786/1‑90 (MQ=255)
aTTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGa > 1:969772/1‑90 (MQ=255)
ttGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGat > 1:1155925/1‑90 (MQ=255)
tGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGata < 2:949251/90‑1 (MQ=255)
ggCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGatat < 2:833573/90‑1 (MQ=255)
ggCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGatat < 1:372737/90‑1 (MQ=255)
ggCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGatat < 1:975117/90‑1 (MQ=255)
gATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTc > 2:405293/1‑90 (MQ=255)
tACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTccc > 2:480033/1‑90 (MQ=255)
aCGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAt > 1:718959/1‑90 (MQ=255)
aCGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAt > 2:1175490/1‑90 (MQ=255)
aCGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAt > 2:41950/1‑90 (MQ=255)
gcgcCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGatat < 1:347288/75‑1 (MQ=255)
gcgcCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGatat > 2:347288/1‑75 (MQ=255)
gcgcCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAtggtgg > 2:766373/1‑90 (MQ=255)
aaGTCCTACTGCTCAGTGAACGTGATGAACCCCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACcgccgc < 1:912415/90‑1 (MQ=255)
aaGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACcgccgc > 2:1103512/1‑90 (MQ=255)
aaGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACcgccgc < 2:916825/90‑1 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTggg < 2:983904/45‑1 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTggg > 1:983904/1‑45 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 2:293618/90‑1 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc < 1:1224480/90‑1 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc > 1:1065529/1‑90 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCcgcg > 2:1108807/1‑90 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCcgca > 2:1012578/1‑89 (MQ=255)
cGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGaa > 2:936713/1‑90 (MQ=255)
tgaACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGc < 2:495304/90‑1 (MQ=255)
ccTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCa < 2:228195/88‑1 (MQ=255)
ccTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCa > 1:228195/1‑88 (MQ=255)
ttCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCa < 1:224444/90‑1 (MQ=255)
cTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGt < 2:1059510/90‑1 (MQ=255)
|
ACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGT > NZ_CP009273/2003394‑2003556
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ 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
TCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC > NZ_CP009273/2003388‑2003566
|
TCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGA > SRR3722089.472364/1‑100 (MQ=60)
TCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGA > SRR3722089.984085/1‑100 (MQ=60)
CCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGAT > SRR3722089.1173518/1‑100 (MQ=60)
ACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCT < SRR3722089.1215958/100‑1 (MQ=60)
CCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCC < SRR3722089.716381/100‑1 (MQ=60)
GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT < SRR3722089.377310/100‑1 (MQ=60)
GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT > SRR3722089.728304/1‑100 (MQ=60)
GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT < SRR3722089.989518/100‑1 (MQ=60)
GACAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT < SRR3722089.351605/100‑1 (MQ=60)
AAGTCCTACTGCTCAGTGAACGTGATGAACCCCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGC < SRR3722089.925699/100‑1 (MQ=60)
GTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCtgtctcttatacacatctgacgctgccgacgacc > SRR3722089.998490/1‑66 (MQ=60)
GTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCC > SRR3722089.1081525/1‑100 (MQ=60)
TCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAC < SRR3722089.1243087/100‑1 (MQ=60)
GTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAAC > SRR3722089.231093/1‑100 (MQ=60)
TTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTT < SRR3722089.227292/100‑1 (MQ=60)
CTGGACCCGGTTTCCGGGGGATATCCCCCCGGATGGTGGGATAACCCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC < SRR3722089.624265/100‑1 (MQ=60)
|
TCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC > NZ_CP009273/2003388‑2003566
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
