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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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 | 95.7%
| 64.6
/ ‑3.2
| 23 | F60S (TTC→TCC) | yedK | SOS response‑associated peptidase |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (16/6); total (17/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.13e-01 |
AACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGT > NZ_CP009273/2003393‑2003560
|
aaCCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCt < 2:265939/90‑1 (MQ=255)
cATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTgggg > 2:189851/1‑90 (MQ=255)
cATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTgggg > 1:619658/1‑90 (MQ=255)
tGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGata < 2:619658/90‑1 (MQ=255)
aCGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAt > 1:322808/1‑90 (MQ=255)
aCGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAt > 1:524656/1‑90 (MQ=255)
aCGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAt > 1:600002/1‑90 (MQ=255)
cgcgCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAtggtg > 2:84641/1‑90 (MQ=255)
ccTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCt < 1:381789/50‑1 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc > 2:46020/1‑90 (MQ=255)
tCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGccc > 2:662354/1‑90 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCcgcg > 2:284894/1‑90 (MQ=255)
gTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCcgcg > 2:671026/1‑90 (MQ=255)
cGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGaa > 2:238498/1‑90 (MQ=255)
tgatgaACCCCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAc < 1:702865/90‑1 (MQ=255)
gatgaACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACt > 2:556805/1‑90 (MQ=255)
tgaACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAc > 1:252101/1‑87 (MQ=255)
tgaACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAAc < 2:252101/87‑1 (MQ=255)
ccTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAAc > 1:713512/1‑90 (MQ=255)
ttCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGCAGAAACTGCGGCAACCa > 1:153323/1‑90 (MQ=255)
gATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATg > 1:103049/1‑90 (MQ=255)
gATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATg > 2:616489/1‑90 (MQ=255)
aTCCGGTTTCCGGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGt < 1:126824/90‑1 (MQ=255)
|
AACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGT > NZ_CP009273/2003393‑2003560
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAAC > NZ_CP009273/2003387‑2003578
|
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGG > SRR3722112.629223/1‑100 (MQ=60)
CCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGAT < SRR3722112.117919/100‑1 (MQ=60)
tcggcagcgtcagatgtgtataagagacaGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGC < SRR3722112.386745/71‑1 (MQ=60)
GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGctgtctcttataca > SRR3722112.470339/1‑86 (MQ=60)
GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT > SRR3722112.326614/1‑100 (MQ=60)
GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT > SRR3722112.532393/1‑100 (MQ=60)
GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT > SRR3722112.609192/1‑100 (MQ=60)
GTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGC > SRR3722112.255079/1‑100 (MQ=60)
GTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAAC > SRR3722112.724663/1‑100 (MQ=60)
TGATGAACCCCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACC < SRR3722112.713842/100‑1 (MQ=60)
GATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGCAGAAACTGCGGCAACCA > SRR3722112.155208/1‑100 (MQ=60)
CCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATG > SRR3722112.104335/1‑100 (MQ=60)
ATCCGGTTTCCGGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCT < SRR3722112.128397/100‑1 (MQ=60)
TCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAAC > SRR3722112.368460/1‑100 (MQ=60)
|
ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAAC > NZ_CP009273/2003387‑2003578
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
