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 F29 I1 R1
|
57 |
65.8 |
2790598 |
98.6% |
2751529 |
146.7 |
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 | 93.3%
| 42.7
/ ‑2.5
| 15 | 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 (6/8); total (6/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 93.3%
| 44.6
/ ‑2.9
| 15 | 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 (6/8); total (6/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 93.3%
| 44.6
/ ‑2.9
| 15 | 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 (6/8); total (6/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01 |
ACGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558275‑5558551
|||
aCGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑Agcg > 7:357926/1‑149 (MQ=255)
gAAATTCTGGTCGGCCTGGGCAGCTTTTAGTCGGGCGGGCATGAGCAACTCCTTTTGTCATGTGTCGCCTACAGAATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑TGCGGCCCCGGCAATTTCcgc < 6:112242/149‑1 (MQ=37)
atttatggTCGGCCTGGGCAGCTATTTGTCGGGCGCTCTTTATCTACTGCTTTTTTCATGTGTCGCCGACAGCATAGCAACACGGCTCTGGTGTGGGAGCGGCGTTGTGTCGCTAATGGGCCGATTTGGGGCC‑‑‑CCGGCAATTTCCGCgt < 2:262572/143‑1 (MQ=255)
aaTTCTGGTCGCCCGGGGCAGCGATTAGGCGGGCGGACATGAGCAACTCCTTTTGTCATGTGGCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCTAATGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCgt < 2:117359/149‑1 (MQ=37)
aTTCCGGGCGGCGGGGGCAGCTATTAGGCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATACCAACACCGCTCCGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGAAT‑‑‑AGCGGCCCCGGCAATTTCCGCgtg < 6:284474/149‑1 (MQ=25)
aTTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCgtg > 7:67391/1‑149 (MQ=255)
gCAGCTATTAGTCGGGCGGAAATTAGCAACTCTTTTTGTCATGTGTCGCCTACAGCATAGCAACACCGCTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGAAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTgg < 4:156978/149‑1 (MQ=37)
gATTTGGCGGGCTGTAATGAGCACCTCTTTTTGTCTGTTGTCGCCGACAGCATTGCAACACGGCTCCGTGGGGGGTGGGGCTTTGTGTCCCGAAAGGGCCTCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctg < 8:67391/149‑1 (MQ=255)
cATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTc < 8:357926/149‑1 (MQ=255)
aaTAGCAACACCGCTCTGGTGTGGTTGCGGCCTTGTGTCGCTAATGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACGAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTc < 8:66174/148‑1 (MQ=25)
ccTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgcgcg > 8:292201/1‑147 (MQ=255)
tgtCGCTAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGa < 6:201921/149‑1 (MQ=38)
tCGCGAAAGGGCCGCGT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCATGCTGGCGCGCAGCTGAgc > 7:335796/1‑149 (MQ=38)
tCGCGAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTg > 5:5625/1‑125 (MQ=38)
gcgAAAGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccg > 5:305609/1‑149 (MQ=255)
aaGGGCCGCAT‑‑‑AGCGGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 2:248432/1‑146 (MQ=255)
|||
ACGCTGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCAT‑‑‑AGCG‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558275‑5558551
|
| 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
