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 |
|
A3 F1 I2 R1
|
777 |
59.2 |
2955938 |
92.5% |
2734242 |
106.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,645,013 |
C→T |
*771* (TAG→TAA) |
pbpC ← |
penicillin‑insensitive murein repair transglycosylase, inactive transpeptidase domain protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,645,013 | 0 | C | T | 97.3%
| 113.5
/ ‑6.4
| 37 | *771* (TAG→TAA) | pbpC | penicillin‑insensitive murein repair transglycosylase, inactive transpeptidase domain protein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (18/18); minor base A (1/0); total (19/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCTGTTGTTGTCTGTACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCATTCAGAAAC > NC_000913/2644883‑2645145
|
ttCTGTTGTTGTCTGTACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCa > 1:1340362/1‑138 (MQ=255)
ttCTGTTGTTGTCTGTACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCa < 2:1340362/138‑1 (MQ=255)
gtCTGTAACATCGTACGAGATGGCGCCGATTATAATGAGCAACAGGGCCAATCCTTATAGTGGAAGGGAACATTTTATTAAAATAAAAAGAGTATTATCATCAATCACAGTCTAAACCGATTATTGAATTGAAAATTTc > 1:1263915/1‑139 (MQ=255)
tACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGt > 1:52345/1‑139 (MQ=255)
cGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCa < 1:1274854/117‑1 (MQ=255)
cGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCa > 2:1274854/1‑117 (MQ=255)
cGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑a > 1:732713/1‑129 (MQ=255)
cGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑a < 2:732713/129‑1 (MQ=255)
gaTGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGcccc < 1:769757/139‑1 (MQ=255)
gcgcGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGt < 2:52345/139‑1 (MQ=255)
aGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGcc < 1:782638/118‑1 (MQ=255)
aGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGAATATTGCATGACAAATTTC‑ACTGTCGCGATTTGcc > 2:782638/1‑118 (MQ=255)
gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCAc > 2:1234972/1‑133 (MQ=255)
gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCAc < 1:1234972/133‑1 (MQ=255)
gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGc > 1:1027893/1‑137 (MQ=255)
gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGc < 2:1027893/137‑1 (MQ=255)
gCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCaa > 1:1117944/1‑139 (MQ=255)
ggCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATaa > 1:775518/1‑139 (MQ=255)
ttGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGGATTTTTACAAAAATCAAGGACAAAAAAGATTTTTTCATTACAAATTTCAACTTTC‑CGATTTTCCCCACGGCCTCCAATCACAGCCAATTaataatacc > 2:1314708/1‑136 (MQ=255)
ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGcccc < 1:1247581/100‑1 (MQ=255)
ttGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGcccc > 2:1247581/1‑100 (MQ=255)
tAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCAc > 2:966008/1‑104 (MQ=255)
tAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCAc < 1:966008/104‑1 (MQ=255)
aaCATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTAt > 1:38118/1‑126 (MQ=255)
aaCATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTAt < 2:38118/126‑1 (MQ=255)
aTTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGt < 2:775518/139‑1 (MQ=255)
ttttAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACg > 2:1341140/1‑85 (MQ=255)
ttttAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACg < 1:1341140/85‑1 (MQ=255)
aatGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCcgcg < 2:741004/139‑1 (MQ=255)
atGAGTTTTAGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGt < 2:1161644/139‑1 (MQ=255)
aGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACg < 2:152755/64‑1 (MQ=255)
aGCAACAATCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACg > 1:152755/1‑64 (MQ=255)
aaTCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCg > 1:311173/1‑139 (MQ=255)
aaTCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCg > 1:1474156/1‑139 (MQ=255)
tCAGGGACAAAACAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGcc < 2:311173/139‑1 (MQ=255)
aaCAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCATTCa < 1:328944/134‑1 (MQ=255)
aaCAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCATTCa > 2:328944/1‑134 (MQ=255)
aaCAGATTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCATTCAGAAac > 1:381773/1‑139 (MQ=255)
|
TTCTGTTGTTGTCTGTACCAGCGTACGAGATGGCGCGGATTATAATGAGCAACAGGGCCGTTGACTATTGATGAAGGTAACATTTTTTTAAAATAAAATGAGTTTTAGCAACAATCAGGGACAAAACAGACTATTGCATGACAAATTTC‑ACTGTCGCGATTTGCCCCACGTCATCC‑ATCACCAGCAATTGATAATCACCTTTATCCGTCAAATGCAGGGTCACGTTGCGCCCGCGTTCAGTTAACGGTTCGCCATTCAGAAAC > NC_000913/2644883‑2645145
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
