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 |
|
A8 F28 I1 R1
|
138 |
62.6 |
2119710 |
99.4% |
2106991 |
138.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,640,492 |
T→C |
T32A (ACT→GCT) |
essQ ← |
Qin prophage; putative S lysis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,640,492 | 0 | T | C | 96.0%
| 70.7
/ ‑6.3
| 25 | T32A (ACT→GCT) | essQ | Qin prophage; putative S lysis protein |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (14/10); total (14/11) |
| Fisher's exact test for biased strand distribution p-value = 4.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTCCTCTCGCAGCCTTACGCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGTTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCATTGATTTCATATCCTCACCCCGATGTACACGGATGGTGCAA > NC_000913/1640375‑1640616
|
ctcctctcGCAGCCTTACGCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAAt < 2:370713/140‑1 (MQ=255)
ctctcGCAGCCTTACGCCTGTCTTCTTTAATCTTGAAATAAAGATTTTTCAGATACGTCACCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGcc > 1:270982/1‑140 (MQ=255)
ctctcGCAGCCTTACGCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGcc > 1:116700/1‑140 (MQ=255)
ttACGCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCa < 2:113398/131‑1 (MQ=255)
ttACGCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCa > 1:113398/1‑131 (MQ=255)
aCGCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCAt > 1:674167/1‑140 (MQ=255)
aCGCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCAt > 2:33594/1‑140 (MQ=255)
gCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTa > 1:334509/1‑140 (MQ=255)
ttcttctTTAATCTTAAAAAAAAGATTTGTCAGATACGTCAGCAGGCAAAAAACCAGGCTCCCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACccg < 2:542619/139‑1 (MQ=255)
gTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACccg > 1:555486/1‑140 (MQ=255)
tcttctTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGaa < 1:963952/125‑1 (MQ=255)
tcttctTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGaa > 2:963952/1‑125 (MQ=255)
cttcttTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACccgcc > 2:117484/1‑140 (MQ=255)
tttaaaTTTTAAAATAAGTTTTTGTCAGAACCGACAGCGGGCAAAAAACGAGGCTACCCAGCACACTGATTGCAGCCCTGTGTGCCGTAGCTATTTTATGGAGTAACTGAAGTGCCCAGAACCCAGCATTACCCGCCGAt < 2:408054/136‑1 (MQ=255)
cttTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGAt > 2:544664/1‑140 (MQ=255)
tCTTAAAAAAAAGATTTGTCAGATCCGTCAGCAGGCAAAAACCCAGGCTCCCCAGCACACCGATTGCACCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAAAAACCAGCATTACCCGCCGATGTGCCa < 1:183645/140‑1 (MQ=255)
aTAAAGATTTGTCAGATACGTCAGCAGGCAAAAACCCAGGCTACCAACCACCCCGATTGCAGCCCACTGTGACGGAGCTTTTTTATCGATTACCTGAAAGGCCAAGAAACCAGCATTCCCCGCCGATGTGCCATAGGCaa < 2:334509/140‑1 (MQ=255)
aaGATTTGTCAGATACGTCAGCAGGCCAAAACCCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAacac < 2:298412/140‑1 (MQ=255)
tGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCtgttg < 1:544664/140‑1 (MQ=255)
cGTCAGCAGGCAAAAAACCAGGCTCCCCAGCACACCGATTGCAGCCCACTGTGACGGAGTTACTTTATCGAGTAACTGAAATGCCCAGAAACCAGCATTCCCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTAt < 1:556768/140‑1 (MQ=255)
cagcagGCAAAAAACCAGGCTCCCCAGCACACCGATTGCACCCCACTGTGACGGAGCTATTTTATCGAGTAACTGCAATCCCCAGAACCCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCa < 2:674167/140‑1 (MQ=255)
gcagGCCAAAAACCAGGCTCCCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTATTTTATCGAGTAACTGCAATGCCCAGAACCCAGCATTCCCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCAtt < 1:931932/140‑1 (MQ=255)
agGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGATAACTTATCCATTGa > 1:772448/1‑140 (MQ=255)
ggCAAAAACCCAGTCAACCCACCACACAAATTGCAGCCCCCTGTGACGGCCCTTATTTATAGAGTAACTCAAATCCCCAAAACCCCACATTCCCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCATTGAt < 2:116700/140‑1 (MQ=255)
aGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCATTGATTTCATATCCTc > 1:957456/1‑140 (MQ=255)
ctccccACCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTACCTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCATTGATTTCATATCCTCAcc < 1:50468/137‑1 (MQ=255)
cTACCCACCACACCGATTCCACCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAAAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGATAACTTATCCATTGATTTCATATCCTCAcc < 2:772448/140‑1 (MQ=255)
cccAGCACACCGATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCATTGATTTCATATCCTCACCCCg < 2:555486/140‑1 (MQ=255)
gATTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCATTGATTTCATATCCTCACCCCGATGTACACGGa > 2:282653/1‑140 (MQ=255)
aTTGCAGCCCACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCATTGATTTCATATCCTCACCCCGATGTACACGGAt > 2:1000817/1‑140 (MQ=255)
agcACTGTGACGGAGCTACTTTATCGAGTAACTGCAATGCCACGAACCCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTCTCCATTGATTTCATATCCTCACCCCGATGTACACGGATGGTGCaa < 2:989187/138‑1 (MQ=255)
|
CTCCTCTCGCAGCCTTACGCCTGTCTTCTTTAATCTTGAAATAAAGATTTGTCAGATACGTCAGCAGGCCAAAAACCAGGCTACCCAGCACACCGATTGCAGCCCACTGTGACGGAGTTACTTTATCGAGTAACTGCAATGCCCAGAAACCAGCATTACCCGCCGATGTGCCATAGGCAACACCTGTTGTTAACTTATCCATTGATTTCATATCCTCACCCCGATGTACACGGATGGTGCAA > NC_000913/1640375‑1640616
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
