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 F13 I1 R1
|
58 |
75.1 |
3211970 |
98.6% |
3167002 |
146.1 |
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 | 90.9%
| 28.3
/ ‑2.8
| 11 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (5/5); total (6/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.48e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 90.9%
| 31.1
/ ‑2.4
| 11 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (5/5); total (6/5) |
| 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 | 3 | . | C | 90.9%
| 30.4
/ ‑2.4
| 11 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (5/5); total (6/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01 |
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGC‑G‑‑‑CC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGAT > NC_002947_CJ‑RC/5558281‑5558556
|||
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgc‑ggcccc < 2:179894/148‑6 (MQ=255)
cACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgc‑ggccccgg > 1:378370/1‑142 (MQ=255)
aCTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgc‑ggccccgg > 5:351797/1‑141 (MQ=255)
gCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTgg < 8:298377/149‑1 (MQ=38)
tttgTCGGGCTGAATTGTGAAACTAGTTTTGTCTTGTGTCGCCTACTTAATACCAACACCGCTCTGTGGTGGTTGGGGACTGGTGTCGCTAAAGGGCCGAATTGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 2:378370/145‑1 (MQ=255)
ggcgcgcgcACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACCCCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt < 6:351797/143‑1 (MQ=37)
aGCAACTCCTTTTGTCATGTGTCGCCTACAGCATAGCAACACCGCTCTGGTGTGGGTGCGGCCTTGTGTCGCTAAAGGGCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 4:201310/149‑1 (MQ=37)
aGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCTGGTGTGGGAGGGGCCTTGTGTCGCTAAAGGGCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGa < 4:300076/149‑1 (MQ=255)
ttGTGTCGCGAAAGGGCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACCCAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 7:256014/1‑149 (MQ=38)
ttGTGTCGCGAAAGGGCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGc > 8:162592/1‑149 (MQ=255)
tCGCGAAAGGGCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 4:82353/1‑149 (MQ=255)
gcgAAAGGGCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGCgccg > 3:120832/1‑149 (MQ=39)
aaGGGCCGCATAGCTG‑‑‑CCAGGGCAATTTCCGCGTGTATGGAACAAACCTGGGGCTGCTATGCAGCACTTTAGCGGGACAAGGCCGACAAAGGACCGCGCAGGGTTCAGGCCGGGAAGTGGGGCAGGATGGCGCGCAGGTGAgccgc > 2:355151/1‑146 (MQ=255)
ggCCGCATAGC‑GGCCCC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGat > 6:372129/1‑148 (MQ=255)
|||
TCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGC‑G‑‑‑CC‑‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGCCAGAT > NC_002947_CJ‑RC/5558281‑5558556
|
| 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
