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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,796,543 |
G→C |
G95G (GGC→GGG) |
thrS ← |
threonine‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,796,543 | 0 | G | C | 76.7%
| 61.8
/ 13.6
| 30 | G95G (GGC→GGG) | thrS | threonine‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base G (3/4); new base C (7/16); total (10/20) |
| Fisher's exact test for biased strand distribution p-value = 6.57e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
TTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCT > NZ_CP009273/1796483‑1796630
|
ttCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAg > 1:153551/1‑90 (MQ=255)
aaCGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATc > 2:837591/1‑90 (MQ=255)
aaCGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATc > 1:135188/1‑90 (MQ=255)
aaCGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATc > 1:520323/1‑90 (MQ=255)
aCGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATcg > 2:146137/1‑90 (MQ=255)
aCGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATcg > 1:370069/1‑90 (MQ=255)
cGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATcgc < 2:143983/90‑1 (MQ=255)
cGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATcgc < 1:582257/90‑1 (MQ=255)
gTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATcgcg < 1:520401/90‑1 (MQ=255)
tGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGt < 1:61774/90‑1 (MQ=255)
gCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCGAAGTTGTTTAATCGCGTg < 2:252581/90‑1 (MQ=255)
gCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTg < 1:478104/90‑1 (MQ=255)
gCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTg < 2:667048/90‑1 (MQ=255)
gCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTg < 2:627845/90‑1 (MQ=255)
gCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTg < 2:436858/90‑1 (MQ=255)
ggTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGcc > 1:319409/1‑90 (MQ=255)
tCAACGTCGTAATAAAAACCGTTGTCAATACCCGGGCCGATTGCCGTTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAgg < 2:690106/90‑1 (MQ=255)
aCGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTgc > 1:696988/1‑90 (MQ=255)
aCGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTg > 1:722067/1‑89 (MQ=255)
aCGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTg < 2:722067/89‑1 (MQ=255)
gtcgtAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTgcgc < 1:408561/90‑1 (MQ=255)
taataaAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAg < 2:319409/90‑1 (MQ=255)
taataaAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAg < 2:422801/90‑1 (MQ=255)
aCCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACg < 2:54855/90‑1 (MQ=255)
gTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAAt > 1:657803/1‑90 (MQ=255)
ttGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATg < 1:835268/90‑1 (MQ=255)
ttGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATg < 1:640316/90‑1 (MQ=255)
tGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGa < 2:426653/90‑1 (MQ=255)
ccGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGAc < 2:455673/90‑1 (MQ=255)
ccGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGAc < 2:716063/90‑1 (MQ=255)
gggCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACct > 1:246412/1‑90 (MQ=255)
|
TTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCT > NZ_CP009273/1796483‑1796630
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ 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
CTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCTTCTTC > NZ_CP009273/1796473‑1796635
|
CTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAG > SRR3722079.154882/1‑100 (MQ=60)
TTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATC > SRR3722079.525123/1‑100 (MQ=60)
TTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATC > SRR3722079.136330/1‑100 (MQ=60)
TCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCG > SRR3722079.373032/1‑100 (MQ=60)
GTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCC > SRR3722079.321979/1‑100 (MQ=60)
CGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAAC < SRR3722079.588019/100‑1 (MQ=60)
GTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACA < SRR3722079.525201/100‑1 (MQ=60)
TGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAG < SRR3722079.62275/100‑1 (MQ=60)
GCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGG < SRR3722079.482294/100‑1 (MQ=60)
GTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGC > SRR3722079.704337/1‑100 (MQ=60)
GTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGC > SRR3722079.729781/1‑100 (MQ=60)
GTCGTAATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGA < SRR3722079.412043/100‑1 (MQ=60)
AATAAAAACCGTTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAAT > SRR3722079.664627/1‑100 (MQ=60)
TTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGAC < SRR3722079.646914/100‑1 (MQ=60)
TTGTCAATAACCGGCCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGAC < SRR3722079.844208/100‑1 (MQ=60)
GTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCT > SRR3722079.248483/1‑100 (MQ=60)
TAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCTTCTTC > SRR3722079.2520/1‑100 (MQ=60)
|
CTTCGACATCTTCCTGGGTTAACGTGCGGTCAAGATCAACGTCGTAATAAAAACCGTTGTCAATAACCGGGCCGATTGCCATTTTGGTATGCGGCCAAAGTTGTTTAATCGCGTGCCCTAACAGGTGCGCACAGGAGTGACGAATGATCTCCAGACCTTCTTC > NZ_CP009273/1796473‑1796635
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
