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 F2 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,629,389 |
(T)8→7 |
intergenic (+42/+18) |
creD → / ← arcA |
cell envelope integrity protein CreD/two‑component system response regulator ArcA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,629,382 | 0 | T | . | 79.0%
| 34.8
/ 12.8
| 19 | intergenic (+35/+25) | creD/arcA | cell envelope integrity protein CreD/two‑component system response regulator ArcA |
| Reads supporting (aligned to +/- strand): ref base T (3/1); new base . (5/10); total (8/11) |
| Fisher's exact test for biased strand distribution p-value = 2.62e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.94e-01 |
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGA > NZ_CP009273/4629303‑4629459
|
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:433566/90‑5 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:800744/90‑5 (MQ=255)
aagTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTaa < 1:282718/90‑1 (MQ=255)
aagTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTaa < 1:437059/90‑1 (MQ=255)
cAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGa < 1:319505/90‑1 (MQ=255)
cGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTa < 1:493469/90‑1 (MQ=255)
gACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt > 1:473699/1‑90 (MQ=255)
gACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt > 1:509870/1‑90 (MQ=255)
gACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt < 1:640190/90‑1 (MQ=255)
ttACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGa > 2:721704/1‑90 (MQ=255)
ttACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGAt > 2:887710/1‑90 (MQ=255)
tACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATc < 2:15199/90‑1 (MQ=255)
tACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATc < 2:505433/90‑1 (MQ=255)
tCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGc > 2:808726/1‑90 (MQ=255)
aaaTAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGc > 2:681189/1‑90 (MQ=255)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa > 2:171579/1‑79 (MQ=255)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa < 1:171579/79‑1 (MQ=255)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCtt > 2:558112/1‑90 (MQ=255)
aaaaaTAAAAACGGCGCTAAAAATCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCa < 1:326651/90‑1 (MQ=255)
aaCGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAAtg < 1:641998/90‑1 (MQ=255)
cTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCga < 2:856122/90‑1 (MQ=255)
|
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGA > NZ_CP009273/4629303‑4629459
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAG > NZ_CP009273/4629303‑4629483
|
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722072.441455/100‑1 (MQ=60)
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722072.814731/100‑1 (MQ=60)
AAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAA < SRR3722072.287556/100‑1 (MQ=60)
AAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAA < SRR3722072.445027/100‑1 (MQ=60)
AGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAT > SRR3722072.482335/1‑100 (MQ=60)
AGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAT > SRR3722072.519045/1‑100 (MQ=60)
CAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCC < SRR3722072.325096/100‑1 (MQ=60)
CGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGA < SRR3722072.502387/100‑1 (MQ=60)
GACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATC < SRR3722072.651611/100‑1 (MQ=60)
GGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACC < SRR3722072.174545/100‑1 (MQ=60)
AAAAATAAAAACGGCGCTAAAAATCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGG < SRR3722072.332383/100‑1 (MQ=60)
AACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGA < SRR3722072.653447/100‑1 (MQ=60)
TTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAG > SRR3722072.750172/1‑100 (MQ=60)
|
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAG > NZ_CP009273/4629303‑4629483
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
