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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
508,601 |
(C)6→7 |
coding (570/1293 nt) |
ybaT → |
APC family permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 508,595 | 1 | . | C | 100.0%
| 73.9
/ NA
| 23 | A188A (GCG→GCC) | ybaT | APC family permease |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (12/11); total (12/11) |
CCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCG > NZ_CP009273/508508‑508679
|
ccTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑cc < 1:585313/90‑1 (MQ=255)
cgtcgGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑ccccc < 2:346515/90‑1 (MQ=255)
aaaaTGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCgg < 2:674556/90‑1 (MQ=255)
atgatgATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGc < 2:593985/90‑1 (MQ=255)
atgatgATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGc < 1:386312/90‑1 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt > 1:130076/1‑90 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt > 2:529775/1‑90 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt > 2:523381/1‑90 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt > 1:77938/1‑90 (MQ=255)
gatgatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGt < 1:245782/90‑1 (MQ=255)
gatCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttct < 2:505169/90‑1 (MQ=255)
tGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTcc < 1:223513/90‑1 (MQ=255)
tGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTcc > 1:124834/1‑90 (MQ=255)
ttGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTAt < 2:363258/90‑1 (MQ=255)
tGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTAtt > 2:515283/1‑90 (MQ=255)
gCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTg > 1:135996/1‑90 (MQ=255)
attattGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttct < 1:402761/74‑1 (MQ=255)
attattGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGttct > 2:402761/1‑74 (MQ=255)
attattGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGAt > 1:545477/1‑90 (MQ=255)
ttattGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATa < 1:529775/90‑1 (MQ=255)
attGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTAGGATAAc < 2:425693/90‑1 (MQ=255)
tgtCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTg > 2:327853/1‑90 (MQ=255)
tCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGcc < 2:545477/90‑1 (MQ=255)
aCCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTg > 2:169578/1‑90 (MQ=255)
ctGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACgcggcg > 1:547278/1‑90 (MQ=255)
|
CCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCG > NZ_CP009273/508508‑508679
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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
CCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGAT > NZ_CP009273/508508‑508694
|
CCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTC < SRR3722112.594253/100‑1 (MQ=60)
GCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGT > SRR3722112.131690/1‑100 (MQ=60)
GCACTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGT > SRR3722112.78884/1‑100 (MQ=60)
ATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCC > SRR3722112.126380/1‑100 (MQ=60)
ATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCC < SRR3722112.391338/100‑1 (MQ=60)
GATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTG < SRR3722112.248694/100‑1 (MQ=60)
agacagGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTAT < SRR3722112.408071/94‑1 (MQ=60)
TCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTG > SRR3722112.137691/1‑100 (MQ=60)
TGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGA < SRR3722112.226201/100‑1 (MQ=60)
GTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGAT > SRR3722112.553676/1‑100 (MQ=60)
TTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTG < SRR3722112.537620/100‑1 (MQ=60)
ATTTCCGTCTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCG > SRR3722112.555524/1‑100 (MQ=60)
CTCTGCGCCCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGT > SRR3722112.502596/1‑100 (MQ=60)
C‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGAT > SRR3722112.566003/1‑100 (MQ=60)
|
CCTCGTCGGCATTAAAATGATGATCCTGTTATTGCTGATTATTGCCGGTGTCTGGTCGCTGCAACCGGCGCATATTTCCGTCTCTGCG‑CCCCCCAGCTCCGGTGCGTTCTTCTCCTGTATTGGGATAACTTTCCTTGCCTATGCGGGCTTTGGCATGATGGCGAACGCGGCGGATAAAGTGAAAGAT > NZ_CP009273/508508‑508694
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
