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 F4 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
469,392 |
T→C |
L324P (CTC→CCC) |
amtB → |
ammonium transporter AmtB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 469,392 | 0 | T | C | 95.2%
| 60.9
/ ‑3.0
| 21 | L324P (CTC→CCC) | amtB | ammonium transporter AmtB |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (13/7); total (14/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.96e-01 |
ACTGCTGGGGGCGTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGGGCGGCGTGGG > NZ_CP009273/469258‑469509
|
aCTGCTGGGGGCGTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCaaa > 2:104794/1‑139 (MQ=255)
ggCGTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTtgctg > 1:291651/1‑139 (MQ=255)
gtgtTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCgg > 2:144066/1‑139 (MQ=255)
tgtTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCggg < 1:80709/139‑1 (MQ=255)
gtTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCCAACGCTTGCTGCgggg > 2:354299/1‑138 (MQ=255)
gtTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCgggg > 1:89926/1‑138 (MQ=255)
aTTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCt > 1:201554/1‑139 (MQ=255)
aTTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCt > 2:299800/1‑139 (MQ=255)
tCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCgg < 2:201554/139‑1 (MQ=255)
cATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGt < 2:291651/138‑1 (MQ=255)
ggggTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGc < 1:299800/138‑1 (MQ=255)
ggcggcGCGTTGATTATCGGCGTGGTAGCTGGTCTGGAGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGGGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCa > 1:414484/1‑139 (MQ=255)
cGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGt < 1:154956/108‑1 (MQ=255)
cGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGt > 2:154956/1‑108 (MQ=255)
cGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGGTTGTGGCATTGTCGGCTGTATCATGACCGGGGTTTTTgccgcc > 2:298878/1‑139 (MQ=255)
tGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAg > 1:419550/1‑139 (MQ=255)
tGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAg > 2:57253/1‑139 (MQ=255)
gTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCCTGACCGGGATTTTTGCCGCCAGCt > 1:85032/1‑139 (MQ=255)
gTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGc < 1:144066/138‑1 (MQ=255)
tCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGggc > 1:60000/1‑139 (MQ=255)
gCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGGGCGGCGTggg < 1:143428/139‑1 (MQ=255)
|
ACTGCTGGGGGCGTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGGGCGGCGTGGG > NZ_CP009273/469258‑469509
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCACTGCTGGGGGCGTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGGGCGGCGTGGGCTTCGCTGAAG > NZ_CP009273/469256‑469520
|
TCACTGCTGGGGGCGTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGC > SRR3722119.294635/1‑151 (MQ=60)
GCTGGGGGCGTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGGG > SRR3722119.90808/1‑151 (MQ=60)
GTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCC < SRR3722119.81484/151‑1 (MQ=60)
GTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGGGGATGATCCCTG > SRR3722119.203703/1‑151 (MQ=60)
ggagatgtgtataagagacaGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCA < SRR3722119.156542/131‑1 (MQ=60)
ACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGAGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGGGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCAT > SRR3722119.418664/1‑151 (MQ=60)
TGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGAC < SRR3722119.302872/150‑1 (MQ=60)
GATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGC > SRR3722119.423763/1‑151 (MQ=60)
TTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGGGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCCTGACCGGGGTTTTTGCCGCCAGCTC > SRR3722119.85856/1‑151 (MQ=60)
GTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGGGCG > SRR3722119.60560/1‑151 (MQ=60)
GGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGGGCGG < SRR3722119.145555/150‑1 (MQ=60)
GGCTTGTGGGGCGTTACCATGCCCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGGGCGGCGTGGGCTTCGCTGAAG < SRR3722119.144911/151‑1 (MQ=60)
|
TCACTGCTGGGGGCGTGTTCTGGCGCGATTGCCGGTCTGGTCGGCGTGACGCCAGCCTGCGGCTACATTGGGGTTGGCGGCGCGTTGATTATCGGCGTGGTAGCTGGTCTGGCGGGCTTGTGGGGCGTTACCATGCTCAAACGCTTGCTGCGGGTGGATGATCCCTGCGATGTCTTCGGTGTGCACGGCGTTTGTGGCATTGTCGGCTGTATCATGACCGGGATTTTTGCCGCCAGCTCGCTGGGCGGCGTGGGCTTCGCTGAAG > NZ_CP009273/469256‑469520
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
