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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,108,830 |
A→G |
H143H (CAT→CAC) |
rraA ← |
ribonuclease E activity regulator RraA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,108,830 | 0 | A | G | 100.0%
| 67.0
/ NA
| 20 | H143H (CAT→CAC) | rraA | ribonuclease E activity regulator RraA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/8); total (12/8) |
GAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAC > NZ_CP009273/4108743‑4108906
|
gAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTg > 2:429339/1‑90 (MQ=255)
aaaaGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTc < 1:270524/90‑1 (MQ=255)
ccTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑gaga > 2:452388/1‑90 (MQ=255)
tCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAGAAGAAGGTGACACCGCCa > 2:310303/1‑90 (MQ=255)
atatCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGAcg > 2:10791/1‑90 (MQ=255)
atatCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGAcg < 2:111291/90‑1 (MQ=255)
tatCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGAcgc < 1:645520/90‑1 (MQ=255)
cAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGAc > 2:295575/1‑90 (MQ=255)
gCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACAt < 1:463693/90‑1 (MQ=255)
gCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACAt > 2:347624/1‑90 (MQ=255)
gATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGc > 1:331289/1‑90 (MQ=255)
tcttctGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCtt < 1:750660/90‑1 (MQ=255)
aaGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAAt > 2:478448/1‑90 (MQ=255)
aaGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAAt > 1:488378/1‑90 (MQ=255)
cccGGTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGcc < 1:739572/90‑1 (MQ=255)
ggTATTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGc > 2:287316/1‑90 (MQ=255)
aTTGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGc > 1:315698/1‑90 (MQ=255)
ttGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCa < 1:21457/90‑1 (MQ=255)
ttGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCa > 2:536836/1‑90 (MQ=255)
tGTCGGCATAAAGGTGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAc < 1:235349/90‑1 (MQ=255)
|
GAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCG‑‑GAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCAC > NZ_CP009273/4108743‑4108906
|
| 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
CAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCGCCAT > NZ_CP009273/4108732‑4108925
|
CAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGT < SRR3722073.719123/100‑1 (MQ=60)
AAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAG < SRR3722073.276246/100‑1 (MQ=60)
ATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGC > SRR3722073.338332/1‑100 (MQ=60)
TATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCT < SRR3722073.658819/100‑1 (MQ=60)
GCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCC < SRR3722073.473590/100‑1 (MQ=60)
GATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAAT > SRR3722073.498750/1‑100 (MQ=60)
TCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGC < SRR3722073.765865/100‑1 (MQ=60)
TAATCCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGC > SRR3722073.322387/1‑100 (MQ=60)
CCCGGTATTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCA < SRR3722073.754549/100‑1 (MQ=60)
TTGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAA < SRR3722073.21999/100‑1 (MQ=60)
TGTCGGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAAT < SRR3722073.240271/100‑1 (MQ=60)
GGCATAAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCC > SRR3722073.621171/1‑100 (MQ=60)
GCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCG > SRR3722073.358170/1‑100 (MQ=60)
AAAGGTGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCGCCAT > SRR3722073.483035/1‑100 (MQ=60)
|
CAGGTAACGCAGAAAAAAGGCACCTTGCGGTGCCTTTCTTATCATTCAATATCCAGCGGATCTTCTGAAAGAATAATCCCGGTATTGTCGGCATAAAGATGGTCGCCGGAGAAGAAGGTGACACCGCCAAAATTGACGCGGACATCGCTTTCGCCAATGCCTTCGCCAGCGGCACCAACCGGAATTGCCGCCAT > NZ_CP009273/4108732‑4108925
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
