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 |
|
A4 F30 I1 R1
|
57 |
69.7 |
2993452 |
98.5% |
2948550 |
147.2 |
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 | 83.3%
| 18.8
/ 1.9
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base G (4/6); total (5/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.18e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 83.3%
| 30.9
/ 1.2
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (4/6); total (5/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 83.3%
| 30.9
/ 1.2
| 12 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (4/6); total (5/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558281‑5558551
|||
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑gcggcccc < 8:240460/148‑6 (MQ=255)
aCTGTGCTGTAAATTCCGGGCGGCCTGGGCAGCGATTAGTCGGGCGGACTTGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGTTGCGGCCTTGTGTCGCGAATGGGCCGCAT‑‑‑A‑‑‑gcggccccgg < 6:270559/148‑8 (MQ=255)
aCTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCGTAAGGGCCGCAT‑‑‑A‑‑‑gcggccccgg < 7:156047/148‑8 (MQ=255)
aGGAAATTCCGGCCGGCCGGGGCAGCGATTAGTCGGGCGCACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAACGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTcc < 4:314126/149‑1 (MQ=37)
aGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTcc > 5:246/1‑149 (MQ=255)
ggCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGc < 2:327171/149‑1 (MQ=38)
ggACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCt < 6:246/149‑1 (MQ=255)
ttaGCAACTCCTTTTGTCTTGTGGCGCCGAAAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGCCGCGAAAGGGCCGCAT‑‑‑T‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 6:295122/147‑1 (MQ=255)
ccAACTCCTTTTGTCATGTGCCCCGTACAGCATAGAAACACCGCTCTGGTGTGGTTGCGGCCTTGTGTCGCTAATGGGCCGAAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGac < 2:127012/148‑1 (MQ=255)
aTGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGACCTTGTGTAGCGAAAGGGCCCCAT‑‑‑ATCGGCC‑‑‑CCCGCAAATTGCGCCTGTATGGAACAAACCAGGGGCGGCGAAGCCGCCCGTTCGCGACACCAGGCCCACAAAg > 7:189234/1‑149 (MQ=255)
gtggCGCCGAACGCATAGAAACCCCGGGCTGGTGTGGTCGCGGCCTTGTGCCCCGAACGGCCCGAATCGGG‑‑‑GCC‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAgg < 6:91480/148‑1 (MQ=255)
tggggCCTGGTGTCGCTAATGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgc < 6:177807/146‑1 (MQ=38)
gcgAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 4:171876/1‑149 (MQ=255)
gcgAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 8:8593/1‑149 (MQ=255)
gAAAGGGCCGCAT‑‑‑A‑‑‑GCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGcgccgc > 4:45219/1‑148 (MQ=39)
|||
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑A‑‑‑GCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558281‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
