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 |
|
A2 F43 I1 R1
|
60 |
76.0 |
3234326 |
98.3% |
3179342 |
146.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,423 |
+GCC |
intergenic (‑84/+87) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,423 | 1 | . | G | 92.3%
| 32.3
/ ‑6.0
| 13 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base G (6/6); minor base C (0/1); total (6/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0%
| 40.9
/ NA
| 13 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (6/7); total (6/7) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 100.0%
| 40.8
/ NA
| 13 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (6/7); total (6/7) |
ACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCC > NC_002947_CJ‑RC/5558283‑5558552
|||
aCTGTGCAGGAAATTCCGGGCGGCCTGGGCAGCTATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgcggccccgg < 1:8103/148‑8 (MQ=38)
aaTTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCgt < 7:117625/149‑1 (MQ=38)
ggCATCTATTCGTGGGGCGTACTTTACCAACTCATTTTTTCTTGTGGCGCCTAAATAATACAAACCCCCCTCTGGTGTGGTCGCGGCCTTGTGTCGCTAATGGGCCGAATAGCGCCCCCGGCAATTTCCGCGTGTATGCAACAAACCTg < 2:184366/149‑1 (MQ=255)
gCAGCGATTCGTCGGGCGGACATGAGAAACTCATTTTGTCAGGTGCCGCCGACAGCATAGCAACCCCGCTCCGGTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 4:204568/149‑1 (MQ=25)
ttAGCCGGGCTGACATGAGCAACTCCTTTTGTCTTGTGTCGCCGACAGCATAGCAACACCCCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 2:384748/148‑1 (MQ=37)
tCGGGCGGAAATGAGCAACTCCTTTTGTCATGTTTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGc < 6:283084/149‑1 (MQ=38)
gCAACTCCTTTTGTCATGGGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGac < 6:160254/149‑1 (MQ=38)
aTGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc > 3:286940/1‑131 (MQ=38)
aTGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 4:286940/131‑1 (MQ=38)
tgtCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCt > 7:185638/1‑147 (MQ=255)
tgtCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAACGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCt > 5:383682/1‑147 (MQ=38)
tCGCGAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTgcgc > 2:341585/1‑149 (MQ=38)
gcgAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTAGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 2:207748/1‑149 (MQ=255)
gAAAGGGCCGCATAGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGCCACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgcc > 3:154128/1‑149 (MQ=255)
|||
ACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCC > NC_002947_CJ‑RC/5558283‑5558552
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
