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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,505,986 |
T→C |
intergenic (‑283/+7) |
BW25113_RS17530 ← / ← trpS |
GntR family transcriptional regulator YhfZ/tryptophan‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,505,986 | 0 | T | C | 100.0%
| 73.7
/ NA
| 23 | intergenic (‑283/+7) | BW25113_RS17530/trpS | GntR family transcriptional regulator YhfZ/tryptophan‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (14/9); total (14/9) |
TTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCT > NZ_CP009273/3505905‑3506062
|
ttGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAAtt > 1:21540/1‑90 (MQ=255)
ttGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAAtt > 1:34500/1‑90 (MQ=255)
ttGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAAtt > 2:248903/1‑90 (MQ=255)
tgtgCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTc < 2:323490/90‑1 (MQ=255)
tgtgCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTc < 2:134871/90‑1 (MQ=255)
aTTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCcac > 2:92169/1‑90 (MQ=255)
aTTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCcac > 2:304234/1‑90 (MQ=255)
ttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAAcc > 2:351969/1‑90 (MQ=255)
tAGCCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAAt < 2:382043/90‑1 (MQ=255)
ggCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCg < 2:3841/90‑1 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt > 1:149488/1‑90 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt > 2:385587/1‑90 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt > 1:54047/1‑90 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt > 1:11759/1‑90 (MQ=255)
tCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCtt > 1:344875/1‑90 (MQ=255)
ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc < 2:149488/90‑1 (MQ=255)
ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc < 2:11759/90‑1 (MQ=255)
gcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGt < 2:358768/90‑1 (MQ=255)
aaCAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTg > 2:197410/1‑90 (MQ=255)
aaGCGCAATTTGCCAGCAACAGTGAATTACGGCTTc > 2:329499/1‑36 (MQ=38)
aaGCGCAATTTGCCAGCAACAGTGAATTACGGCTTc < 1:329499/36‑1 (MQ=38)
aaGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTgcgcg > 2:385363/1‑90 (MQ=255)
aaTTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCt < 1:385363/90‑1 (MQ=255)
|
TTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCT > NZ_CP009273/3505905‑3506062
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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
CTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGC > NZ_CP009273/3505895‑3506072
|
CTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATT > SRR3722091.21839/1‑100 (MQ=60)
CTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATT > SRR3722091.34989/1‑100 (MQ=60)
cactaagatggtcgtcggcagcgtcagatgtgtataagagacagGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAAC < SRR3722091.335206/56‑1 (MQ=60)
ACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCT > SRR3722091.11929/1‑100 (MQ=60)
ACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCT > SRR3722091.151691/1‑100 (MQ=60)
ACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCT > SRR3722091.54852/1‑100 (MQ=60)
GATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTT > SRR3722091.350918/1‑100 (MQ=60)
AATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGC < SRR3722091.392162/100‑1 (MQ=60)
|
CTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGC > NZ_CP009273/3505895‑3506072
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
