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 |
|
A0 F0 I1 R1
|
52 |
69.5 |
2964196 |
98.4% |
2916768 |
145.9 |
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 | 91.7%
| 27.8
/ ‑5.3
| 13 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); major base G (3/8); minor base C (0/1); total (3/10) |
| 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 | 92.3%
| 38.3
/ ‑2.9
| 13 | 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 (3/9); total (3/10) |
| 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 | 83.3%
| 28.0
/ 1.2
| 13 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (3/7); total (3/10) |
| 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 |
TGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGC > NC_002947_CJ‑RC/5558279‑5558548
|||
tGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggccc > 1:264999/1‑145 (MQ=255)
tCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcggcccc < 4:184363/148‑6 (MQ=255)
gggCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCTCC‑GGCAATTTCCGCGTGTATGCAACAAACCt < 1:154530/149‑1 (MQ=255)
gCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTgg > 7:323441/1‑149 (MQ=255)
ggcGGGCGCACATGAGCAACTCCTTTTGTCAGGTGGCGCCGACAGCATAGCAACACCGCTCTGGGGTGGGCGCGGCGTTGGGTCGCGAACGGCCCGCAT‑‑‑AGCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt < 6:113352/146‑1 (MQ=255)
ggCGTACTTGAGCAACTCCTTTTGTCTTGTGTCGCCTAAAGAATAGCAACACCGCTCCGGTGGGGGAGCGGCCTTGTGTCGCTAAAGGGCCGAAT‑‑‑AGCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGc < 6:311680/149‑1 (MQ=255)
ggCGGACTTGAGCAACTCCTTTTGTCTTGTGTCGCCGACAGAATAGCAACACCGCTCTGGTGTGGGAGCGGCGTTGTGTCGCTAAAGGGCCGCAT‑‑‑AGCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGc < 8:230386/149‑1 (MQ=255)
gCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGcc < 8:323441/149‑1 (MQ=255)
aCATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCC‑GGCAATTTCCGCGTGTATGca > 1:271124/1‑120 (MQ=37)
gagaAACTCTTTTTGTAATGTGTCGCCGACAGAATAGCAACACCGCTCTGGTGTGGGAGCGGCTTTGTGTCGCTAATGGGCCGAAT‑‑‑AGCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGTAGCCCTTTcgc < 8:20993/148‑1 (MQ=255)
gtattgtgtgGCCGACAGAATATAAAAACCGCTCTGTTGTGGTTGGGGGTTTTTGTCGCTAATGGGCGGAATTGGGGCC‑‑‑CC‑GGAAATTTCCGGGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCcac < 2:192966/144‑1 (MQ=255)
aaTAGAAACCCGGCTCTGGTGGGGTTGGGGCTTTGTGTCGCTAATGGGCCGAAT‑‑‑AGCGGC‑CCGGGCAATTTCCGCGTTTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCtt < 8:185391/147‑1 (MQ=21)
accacccccGCTCTGGTGGGGTTGGGGCTTTGTGTCGCTAATGGGCCGAAT‑‑‑CGCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTTCTATGCAGCCCTTTCGCTAAACAAGGCCCACAAAGGACCGCGCAGGCTTCAgg < 8:366941/142‑1 (MQ=255)
cggtgggggtgggGCTTTGTGCCGCGAATGGGCCTAAT‑‑‑CGCGCCCCC‑GGCAATTTCCGCGTTTATGCAACAACCCTGGGGCGGCAATGCAGCCCTTGCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTgg < 8:224172/146‑1 (MQ=255)
tCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgc > 1:17207/1‑149 (MQ=255)
|||
TGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CC‑GGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGC > NC_002947_CJ‑RC/5558279‑5558548
|
| 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
