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 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
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 | . | 100.0%
| 101.6
/ NA
| 24 | intergenic (+35/+25) | creD/arcA | cell envelope integrity protein CreD/two‑component system response regulator ArcA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (12/12); total (12/12) |
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC > NZ_CP009273/4629303‑4629466
|
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 2:115715/90‑5 (MQ=255)
aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg < 1:613097/90‑5 (MQ=255)
gTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACgg > 1:162104/1‑90 (MQ=255)
agTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTaaa > 2:235412/1‑90 (MQ=255)
cGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTa < 1:41277/90‑1 (MQ=255)
gACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt < 1:221597/90‑1 (MQ=255)
cGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCt < 2:221788/90‑1 (MQ=255)
tGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTcc < 1:127011/90‑1 (MQ=255)
tACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATc > 2:175742/1‑90 (MQ=255)
tCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCa > 1:48548/1‑90 (MQ=255)
cTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAg < 2:392441/90‑1 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa > 1:91079/1‑90 (MQ=255)
tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa < 1:96764/90‑1 (MQ=255)
ggAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGaa < 1:128737/90‑1 (MQ=255)
ggAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGaa < 2:361740/90‑1 (MQ=255)
tAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGAt > 1:112249/1‑90 (MQ=255)
aaGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATa < 1:366399/90‑1 (MQ=255)
aaGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATa < 1:103744/90‑1 (MQ=255)
aGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATaa > 1:272006/1‑90 (MQ=255)
aGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATaa > 2:450241/1‑90 (MQ=255)
tGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCtt > 1:368094/1‑90 (MQ=255)
aaaaaTAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCa < 2:39335/90‑1 (MQ=255)
gcgcTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAAtggtgg > 2:293894/1‑90 (MQ=255)
aaaaaGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCgatg < 1:175742/90‑1 (MQ=255)
gcgcCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTtc > 2:162285/1‑90 (MQ=255)
gcgcCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTtc > 1:188646/1‑90 (MQ=255)
|
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC > NZ_CP009273/4629303‑4629466
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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
ATGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCG > NZ_CP009273/4629294‑4629471
|
ATGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGG > SRR3721989.165050/1‑100 (MQ=60)
AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGC < SRR3721989.626387/100‑1 (MQ=60)
CGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGA < SRR3721989.41982/100‑1 (MQ=60)
GACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGACC < SRR3721989.225608/100‑1 (MQ=60)
TGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGC < SRR3721989.129344/100‑1 (MQ=60)
GAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCA > SRR3721989.49377/1‑100 (MQ=60)
GTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGA > SRR3721989.92728/1‑100 (MQ=60)
TATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGAT > SRR3721989.114297/1‑100 (MQ=60)
TCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAA > SRR3721989.276879/1‑100 (MQ=60)
TGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACC < SRR3721989.98514/100‑1 (MQ=60)
GGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCT < SRR3721989.131098/100‑1 (MQ=60)
GAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTT > SRR3721989.375291/1‑100 (MQ=60)
AAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCG < SRR3721989.105638/100‑1 (MQ=60)
AAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCG < SRR3721989.373540/100‑1 (MQ=60)
GCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC > SRR3721989.192104/1‑100 (MQ=60)
AAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCG < SRR3721989.178961/100‑1 (MQ=60)
|
ATGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCG > NZ_CP009273/4629294‑4629471
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
