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 F5 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
728,467 |
T→C |
I1143I (ATT→ATC) |
rhsC → |
rhs element protein RhsC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 728,467 | 0 | T | C | 100.0%
| 66.1
/ NA
| 21 | I1143I (ATT→ATC) | rhsC | rhs element protein RhsC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (7/14); total (7/14) |
CTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCTGAATGAAGAGAACCCGCATCAGCT > NZ_CP009273/728333‑728592
|
cTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCAc < 2:115191/138‑1 (MQ=21)
cTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCAc < 2:207532/138‑1 (MQ=21)
gACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGt < 1:392396/139‑1 (MQ=21)
gACCGGGGGAGGGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGc < 2:298004/139‑1 (MQ=255)
aCCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGc < 2:393804/138‑1 (MQ=21)
cGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTgg > 1:476754/1‑139 (MQ=21)
tgagGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCg < 1:421796/110‑1 (MQ=25)
tgagGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCg > 2:421796/1‑110 (MQ=25)
agGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCa < 1:78638/138‑1 (MQ=37)
tGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCTCCTGTACCACGGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACg < 2:332277/139‑1 (MQ=255)
tGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACg > 2:536393/1‑139 (MQ=255)
tGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGa < 2:142117/139‑1 (MQ=255)
gcgcAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGaa < 1:63186/138‑1 (MQ=255)
tGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCg < 2:571233/60‑1 (MQ=255)
tGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCg > 1:571233/1‑60 (MQ=255)
aGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACctgc < 2:398449/139‑1 (MQ=255)
aTGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCtgaat > 1:507831/1‑138 (MQ=255)
ggTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCTGAATGAAGAGAAc < 2:408751/139‑1 (MQ=255)
cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGa > 2:480953/1‑100 (MQ=255)
cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGa < 1:480953/100‑1 (MQ=255)
cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCTGAATGAAGAGAACCCGCATCAGCt > 1:419859/1‑139 (MQ=255)
|
CTCGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCTGAATGAAGAGAACCCGCATCAGCT > NZ_CP009273/728333‑728592
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCTGAATGAAGAGAACCCGCATCAGCTG > NZ_CP009273/728335‑728593
|
CGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGAC < SRR3722139.397072/151‑1 (MQ=21)
ggaaagctaactcctgggcgcCCGGGTGAGTGAGGAAAGCCGCCACTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGC < SRR3722139.263968/130‑1 (MQ=21)
agatgtgtataagagacagGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGC < SRR3722139.426769/132‑1 (MQ=22)
TCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGC > SRR3722139.482319/1‑151 (MQ=21)
tttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAG < SRR3722139.178696/77‑1 (MQ=0)
GAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGG < SRR3722139.79545/150‑1 (MQ=42)
GGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaa > SRR3722139.577767/1‑85 (MQ=26)
gtgggctcggagatgtgtataagagacagGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACC < SRR3722139.486556/122‑1 (MQ=55)
GGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCT < SRR3722139.63919/150‑1 (MQ=60)
TGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCTGAATG > SRR3722139.513683/1‑150 (MQ=60)
GGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCTGAATGAAGAGAACCCGCATCAGCTG > SRR3722139.424822/1‑151 (MQ=50)
|
CGACCGGCTGGAAAGTGAAATCCTGGCTGACCGGGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGATGAATGGGGTAACCTGCTGAATGAAGAGAACCCGCATCAGCTG > NZ_CP009273/728335‑728593
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
