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 F79 I1 R1
|
61 |
81.5 |
3485072 |
98.6% |
3436280 |
145.0 |
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 | 95.5%
| 69.2
/ ‑2.7
| 22 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (10/11); total (10/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.09e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 95.5%
| 70.2
/ ‑3.1
| 22 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (10/11); total (10/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 95.5%
| 69.7
/ ‑3.1
| 22 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (10/11); total (10/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01 |
AGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558299‑5558551
|||
aGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggc < 5:429164/127‑3 (MQ=255)
aGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATg < 2:68015/149‑1 (MQ=255)
gcctgCGATTAGCCGGGCGTACTTGAGAACCTCCTTTTGTAATGTGCCGCCGAAAGCATACCAACCCCCCGCAGGTGGGGGTGCGGCCTTGTGTCGCTAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCt < 2:266371/144‑1 (MQ=255)
gCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCTTGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGTAGCGGCCTTGTGTCGCTAATGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 2:71197/149‑1 (MQ=255)
cGATTAGTCGGGCGCACATGAGCAACTCCTTTTGTAATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgct < 8:78521/149‑1 (MQ=38)
ttgggcGGGCGTACATGAGAAACTCCTTTGGTCTTGTGTCGCCTACATCATCGCAACCCGGCTCGGGGGGGGGCGCGGCGTGGTGCCGCTAAGGGCCCGCTTCGGGGCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 4:156556/143‑1 (MQ=255)
aGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTa < 4:354567/148‑1 (MQ=255)
tCGGGCGGACAGGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGc < 4:104441/149‑1 (MQ=38)
ggCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGc < 2:103687/149‑1 (MQ=255)
tGAGCAACTCTTTTTGTCATGTGTCGCCGACAGCATTCCAACACCGCTCTGGTGTGGGTGCGGCCTTGTGTCGCTAATGGGCCGAAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 2:432366/149‑1 (MQ=37)
tGACCAACTCCTTTTTTCTTGTGTGGCCGACTGCATACCAACACCGCTCTGGTGTGGGAGGGGCATTGTGTCGCTAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 2:180281/149‑1 (MQ=255)
tCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg < 8:306095/113‑1 (MQ=37)
tCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgggg > 7:306095/1‑113 (MQ=37)
tgtCGCTGAAAGAATACCAACACCGCTCTGGTGTGGGTGGGGCGTTGTGTCGCTAATGGCCCGAAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTTTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGa < 6:203018/148‑1 (MQ=21)
ttGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 4:163265/1‑149 (MQ=255)
tCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTTTGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCCGCTgcgc > 1:237565/1‑149 (MQ=38)
tCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 7:33903/1‑149 (MQ=255)
tCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 2:181293/1‑149 (MQ=255)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 5:83576/1‑149 (MQ=255)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 1:268314/1‑149 (MQ=255)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 1:168259/1‑149 (MQ=255)
gAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 7:21446/1‑148 (MQ=255)
aGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 4:59517/1‑145 (MQ=255)
|||
AGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558299‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
