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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,056,058 |
T→C |
I449I (ATT→ATC) |
torA → |
trimethylamine‑N‑oxide reductase TorA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,056,058 | 0 | T | C | 93.3%
| 48.1
/ ‑2.2
| 15 | coding (1347/2547 nt) | torA | trimethylamine‑N‑oxide reductase TorA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (10/4); minor base . (1/0); total (11/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.27e-01 |
TTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCT > NZ_CP009273/1055990‑1056141
|
ttCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATg > 2:675838/1‑91 (MQ=255)
ctcCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGATTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCg < 1:814837/91‑1 (MQ=255)
aCGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAAc > 2:747281/1‑91 (MQ=255)
gATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCg > 1:177469/1‑76 (MQ=255)
gATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCg < 2:177469/76‑1 (MQ=255)
gATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCgggg > 2:92179/1‑91 (MQ=255)
ttCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGaa < 1:502152/91‑1 (MQ=255)
cTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGAt < 1:245129/91‑1 (MQ=255)
gTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCa > 2:657083/1‑91 (MQ=255)
acaGTGACTACAAAGGCTACAGCAGCACTAT‑‑‑‑‑‑‑‑CCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCgg > 2:126571/1‑91 (MQ=255)
gACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAAt > 2:693271/1‑91 (MQ=255)
gcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCt > 1:136644/1‑91 (MQ=255)
gcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCt > 1:232919/1‑91 (MQ=255)
gcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCt > 1:561650/1‑91 (MQ=255)
gcaCTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCt > 1:637139/1‑91 (MQ=255)
|
TTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCT > NZ_CP009273/1055990‑1056141
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ 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
GGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGT > NZ_CP009273/1055964‑1056151
|
GGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTCTCCCGATT < SRR3722118.641401/101‑1 (MQ=60)
CTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGATTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAAC < SRR3722118.832760/101‑1 (MQ=60)
GCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCtgtc > SRR3722118.180952/1‑97 (MQ=60)
TTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAAC < SRR3722118.512800/101‑1 (MQ=60)
CTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAAC < SRR3722118.250094/101‑1 (MQ=60)
GGCTCCAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCT > SRR3722118.573554/1‑101 (MQ=60)
GGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCT > SRR3722118.139244/1‑101 (MQ=60)
GGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCT > SRR3722118.237615/1‑101 (MQ=60)
GGCTACAGCAGCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCT > SRR3722118.650883/1‑101 (MQ=60)
GCACTATCCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACtgtctcttatacacatctccgagcccacgagacgga > SRR3722118.522702/1‑65 (MQ=60)
|
GGCGTAAAGGCGTTATTCTGAGTGGTTTCTCCGGCTCTACGTCGATTCCGCCTGTTCACGACAACAGTGACTACAAAGGCTACAGCAGCACTATTCCGATTGCCCGTTTTATCGATGCGATCCTCGAACCGGGGAAAGTGATCAACTGGAACGGTAAATCGGTAAAACTGCCGCCGCTGAAAATGTGT > NZ_CP009273/1055964‑1056151
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
