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 I0 R1
|
203 |
85.6 |
3649704 |
98.8% |
3605907 |
146.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,754,561 |
A→C |
25.2% |
intergenic (‑184/‑287) |
thiI ← / → glnA |
tRNA sulfurtransferase/glutamine synthetase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,754,561 | 0 | A | C | 25.2%
| 46.0
/ 2.7
| 25 | intergenic (‑184/‑287) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| Reads supporting (aligned to +/- strand): ref base A (12/6); new base C (3/2); total (16/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGCGAATTATATCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAACCCGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCACGCAAACGCCCCCT > NC_002947_CJ‑RC/5754416‑5754703
|
gcgcGAATTATATCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAACCCGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGa < 8:67370/146‑1 (MQ=255)
gcgcGAATTATATCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAACCCGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGa > 7:67370/1‑146 (MQ=255)
cgcgAATTATATCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAACCCGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑gg < 2:27904/149‑1 (MQ=255)
aTTATATCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAACCCGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGttt < 5:56990/148‑1 (MQ=255)
tatCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAAACCCCGCCGACAGGCGGGGCAAACCCCCTA‑GGAGCC‑GGGTTTA‑ccg > 2:146082/1‑148 (MQ=255)
atCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAAACCCCGCCGAAAGGGCGGGGAAAGCCCGAAGGGCG‑C‑GGGTTTA‑cccc > 7:75097/1‑148 (MQ=255)
tCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTTAAACCGCGCCGACAGGCGGGGGAAAGCCCGGA‑GGGG‑C‑GGGGTTT‑ACcgcg > 1:293393/1‑149 (MQ=255)
cTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAACACCCGCCTAAACGCGGGGGCAAGCCCCTA‑GGAC‑C‑CGCTTTA‑GCCCCCGAGACGccc > 6:198409/1‑148 (MQ=255)
ccAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGGAAAAACGCCCCAACACGCGGTGCAAAGCCCGGA‑GGAG‑C‑GGGTTTT‑CCCCCCAAGAGGGCCGTGAACCggggcc > 7:223016/1‑146 (MQ=255)
gTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAAACCCCCCCGAAACGCGGTGCAAAACCCCTA‑GGCG‑CGGGGTTTA‑CCC‑CGAAGAGGCCCGAGAACCAGGGACACCACACACCCCCCCCCCCCAAATTGTTCGCCACCATCaaa > 8:223994/1‑148 (MQ=255)
cAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAACCCGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCa < 2:293393/149‑1 (MQ=255)
gcgcGTGTTCC‑GCCC‑TTTCGGCGGGAAAACCCGGGCCAACCGGGGGTGAAAAGCCC‑TA‑CGCA‑G‑GGGTTTACCCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATc < 5:198409/149‑1 (MQ=255)
ttCCGGCCC‑TTTC‑GCGTGTAAACCCGCGCCTACTGGCGGTGAAAAGCCGTTA‑GTAG‑G‑GGGTTTA‑CCCGAGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAgg < 8:446971/148‑1 (MQ=255)
gtgcGGCCCTTTTC‑GCGTGAAACCCGGCGCTTACTGGGGGTTAAATGCCCTTA‑GGGG‑C‑GGTTTAA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAgg < 8:75097/146‑1 (MQ=255)
gcgGTTAACCCCGCGCATACAGGCGTTGAAATGCCCTTT‑GGCG‑G‑GGTTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCAccc < 6:308244/149‑1 (MQ=255)
gcgGGTAAACCCGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCAccc > 3:65618/1‑149 (MQ=255)
ccGCTCCTACGGGCTTTGCACCGCCTGTA‑GGCG‑C‑GGGTTTA‑CCCGCGAA‑AGGGCC‑GGAA‑CAGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGc > 3:322110/1‑149 (MQ=18)
ccGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCaa > 5:224365/1‑149 (MQ=255)
ccGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCaa > 2:109327/1‑149 (MQ=255)
cTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCa > 7:319991/1‑148 (MQ=255)
gCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCAc > 4:345060/1‑149 (MQ=255)
gCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCACGCaaa > 7:213942/1‑149 (MQ=255)
cAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCACGCAAAc < 1:109327/149‑1 (MQ=255)
aaaGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCACGCAAACg > 1:392317/1‑149 (MQ=255)
ccGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCACg > 2:399561/1‑138 (MQ=255)
ccGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCACg < 1:399561/138‑1 (MQ=255)
cGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCACGCAAACGCCCCCt > 3:29391/1‑149 (MQ=255)
|
GCGCGAATTATATCGGAAATTGCTCAGGATTTGACCAACTTTTGATCAGAAGCTTTGAGATAAATGCAGAGGCCAGGTTTTGCAGCGCCTGTTCCGGCCC‑TTTC‑GCGGGTAAACCCGCGCCTACAGGCGGTGCAAAGCCCGTA‑GGAG‑C‑GGGTTTA‑CCCGCGAAGAGGCCCTAGAACCTGGCACACCACTCACGCCACGCACCCTATTGGTGCGACACGATCAAAAAACGCATCGTAAGGGTGCACTTTCACCCGCTAACCCAACGCCAAATGCACGCAAACGCCCCCT > NC_002947_CJ‑RC/5754416‑5754703
|
| 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
