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 F3 I95 R1
|
196 |
14.2 |
808436 |
96.0% |
776098 |
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 | . | 95.0%
| 71.6
/ ‑1.4
| 20 | intergenic (+35/+25) | creD/arcA | cell envelope integrity protein CreD/two‑component system response regulator ArcA |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (8/11); total (8/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01 |
AAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGA > NZ_CP009273/4629297‑4629459
|
aaaGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGttttt > 2:379769/1‑90 (MQ=255)
cAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgac < 1:294331/90‑4 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:151529/90‑5 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:351976/90‑5 (MQ=255)
ttACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGc < 1:269557/90‑1 (MQ=255)
gACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt < 2:206387/90‑1 (MQ=255)
aCGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt > 1:92807/1‑89 (MQ=255)
aCGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt < 2:92807/89‑1 (MQ=255)
tACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATc < 1:177118/90‑1 (MQ=255)
aTCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGc < 1:209905/90‑1 (MQ=255)
tCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCa > 1:161265/1‑90 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa < 1:320274/90‑1 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa > 1:243551/1‑90 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa < 2:20570/90‑1 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa < 2:266098/90‑1 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa > 2:323578/1‑90 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCATCCAGATCACCGCAGa > 2:12124/1‑90 (MQ=255)
aaGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATa < 1:379769/90‑1 (MQ=255)
aaaaTAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCa < 2:36295/90‑1 (MQ=255)
gcgcTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAAtggtgg > 2:15644/1‑90 (MQ=255)
gcgcTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAAtggtgg > 2:181138/1‑90 (MQ=255)
cTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCga < 1:246078/90‑1 (MQ=255)
gcgcCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGa > 1:285134/1‑58 (MQ=255)
gcgcCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGa < 2:285134/58‑1 (MQ=255)
|
AAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGA > NZ_CP009273/4629297‑4629459
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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
CAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGT > NZ_CP009273/4629302‑4629481
|
CAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAG < SRR3722235.298436/100‑1 (MQ=60)
gacagAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722235.240366/95‑1 (MQ=60)
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722235.153257/100‑1 (MQ=60)
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3722235.357046/100‑1 (MQ=60)
GTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATC > SRR3722235.93896/1‑100 (MQ=60)
TTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCT < SRR3722235.273186/100‑1 (MQ=60)
GAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCA > SRR3722235.163120/1‑100 (MQ=60)
GTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGA > SRR3722235.246659/1‑100 (MQ=60)
TACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAG < SRR3722235.179152/100‑1 (MQ=60)
ATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATA < SRR3722235.212494/100‑1 (MQ=60)
TGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACC < SRR3722235.324802/100‑1 (MQ=60)
AAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCG < SRR3722235.385244/100‑1 (MQ=60)
GCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCtgtctcttatacacatctccg > SRR3722235.289071/1‑79 (MQ=60)
CTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGG < SRR3722235.249223/100‑1 (MQ=60)
GTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGT < SRR3722235.107110/100‑1 (MQ=60)
GTTTTTTTGACGGTGGTAAAGCCGATTAATCATCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGT < SRR3722235.12258/100‑1 (MQ=60)
|
CAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGT > NZ_CP009273/4629302‑4629481
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
