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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,855,234 |
Δ1 bp |
coding (356/1077 nt) |
ydjL ← |
zinc‑binding dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,855,231 | 0 | C | . | 90.0%
| 31.0
/ ‑1.3
| 10 | coding (359/1077 nt) | ydjL | zinc‑binding dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base . (5/4); total (5/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCG > NZ_CP009273/1855145‑1855314
|
cAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGccca < 2:177420/90‑2 (MQ=255)
acacCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGcccagg > 1:380629/1‑87 (MQ=255)
cacCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGcccaggt < 2:559111/90‑5 (MQ=255)
tCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGAc > 2:537327/1‑90 (MQ=255)
cATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTAc > 1:185773/1‑90 (MQ=255)
cATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTAc > 1:541612/1‑90 (MQ=255)
aCGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACtttt < 2:185773/90‑1 (MQ=255)
gATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTc < 1:231152/90‑1 (MQ=255)
atatTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGcc > 1:311642/1‑90 (MQ=255)
atatTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGcc < 2:237512/90‑1 (MQ=255)
aaaaCCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAac < 2:217544/90‑1 (MQ=255)
aaaCCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAacac > 2:166297/1‑90 (MQ=255)
accaccG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCg < 2:292793/90‑1 (MQ=255)
|
CAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCG > NZ_CP009273/1855145‑1855314
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTCATAATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCGCAAACGTGACCGCTGTTAT > NZ_CP009273/1855137‑1855333
|
CTCATAATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGG > SRR3722092.387850/1‑100 (MQ=60)
TCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTAC > SRR3722092.188860/1‑100 (MQ=60)
TCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTAC > SRR3722092.552490/1‑100 (MQ=60)
GATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACAC < SRR3722092.234930/100‑1 (MQ=60)
GAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCC > SRR3722092.317147/1‑100 (MQ=60)
GCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCGCAAACGTGACCGCTGT > SRR3722092.102598/1‑100 (MQ=60)
CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCGCAAACGTGACCGCTGTT > SRR3722092.426624/1‑100 (MQ=60)
CAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCGCAAACGTGACCGCTGTTAT > SRR3722092.401043/1‑100 (MQ=60)
|
CTCATAATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCGCAAACGTGACCGCTGTTAT > NZ_CP009273/1855137‑1855333
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
