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 |
|
A10 F28 I1 R1
|
126 |
51.4 |
1736588 |
99.0% |
1719222 |
138.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,528,389 |
G→A |
S596S (AGC→AGT) |
ligA ← |
DNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,528,389 | 0 | G | A | 95.2%
| 65.4
/ ‑4.4
| 21 | S596S (AGC→AGT) | ligA | DNA ligase |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (11/9); minor base C (1/0); total (12/9) |
| 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 |
CGGTTTTCTTCGACACGCTGCCCGCGACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGGCTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCC > NC_000913/2528268‑2528520
|
cGGTTTTCTTCGACACGCTGCCCGCGACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCcgcg < 1:722599/140‑1 (MQ=255)
gACACGCTGCCCGCGACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGAt < 2:112594/140‑1 (MQ=255)
cccGCGACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCg < 1:32985/133‑1 (MQ=255)
cccGCGACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCg > 2:32985/1‑133 (MQ=255)
ccGCGACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGc < 1:56321/140‑1 (MQ=255)
gcgACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCa > 2:138214/1‑140 (MQ=255)
gcgACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCa > 1:730533/1‑140 (MQ=255)
tCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAaca > 1:395664/1‑140 (MQ=255)
cccAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGCTGATAACGATCGGCGCAGGCCAGTGAACACCTTc > 1:820965/1‑140 (MQ=255)
cAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTcc > 2:812281/1‑139 (MQ=255)
cAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTcc < 1:812281/139‑1 (MQ=255)
ccAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGc < 1:618924/140‑1 (MQ=255)
gTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCg > 1:85337/1‑140 (MQ=255)
tCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGCCTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGc > 1:750635/1‑140 (MQ=255)
tCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGc < 1:138214/140‑1 (MQ=255)
cgACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGCTGATGACATTGCGGTTGCttt > 1:125471/1‑140 (MQ=255)
cATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGCTGATGACATTGCGGTTGCTttctt < 1:499703/140‑1 (MQ=255)
cacGGTTTTACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATg > 1:610931/1‑140 (MQ=255)
ttttACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACg > 2:12353/1‑140 (MQ=255)
tACCAGCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACa < 2:85337/140‑1 (MQ=255)
gCAAACGGACTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGcc > 2:615120/1‑140 (MQ=255)
|
CGGTTTTCTTCGACACGCTGCCCGCGACTTTCGCGCCCAGTTCGACCAGTCGAGCTTTAGCGTCATCACGCGACATCTGGCTTAAGCTGCCCGTAAGCACCACGGTTTTACCAGCAAACGGGCTGTCAATCTCTTCCGCGTTGATAACGATCGGCGCAGGCCAGTGAACACCTTCCGCCAACAGCTCGCTGATGACATTGCGGTTGCTTTCTTCGGCAAAGAAGTTGTGAACGTGGGATGCAACGACAATGCC > NC_000913/2528268‑2528520
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
