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 |
|
A2 F5 I181 R1
|
159 |
32.7 |
1279082 |
96.9% |
1239430 |
121.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
693,461 |
T→G |
K391N (AAA→AAC) |
asnB ← |
asparagine synthase B |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 693,461 | 0 | T | G | 96.3%
| 93.3
/ NA
| 27 | K391N (AAA→AAC) | asnB | asparagine synthase B |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (11/15); total (11/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
TCACGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCTTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTTCATCAGAACCTTCACC > NZ_CP009273/693330‑693592
|
tCACGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAGGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTgg > 1:204689/1‑139 (MQ=255)
cACGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTgg < 1:633882/138‑1 (MQ=255)
cGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCAc < 2:511860/139‑1 (MQ=255)
gATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCTCCAGGCTGACATCGCGTTGTTGGCAcgcgcg < 2:172241/139‑1 (MQ=255)
gATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCAcgcgcg < 2:344542/139‑1 (MQ=255)
tgtTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGt < 2:101564/139‑1 (MQ=255)
tgtTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGt < 1:454198/139‑1 (MQ=255)
tCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGt < 2:91446/133‑1 (MQ=255)
tCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGt > 1:91446/1‑133 (MQ=255)
cTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGtc < 1:604053/139‑1 (MQ=255)
gtgGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGtctc > 1:18757/1‑139 (MQ=255)
gtgGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGtctc > 1:446441/1‑139 (MQ=255)
tgGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCcag > 2:314812/1‑120 (MQ=255)
tACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAg > 2:456623/1‑139 (MQ=255)
cATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCg < 1:562263/122‑1 (MQ=255)
cATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCg > 2:562263/1‑122 (MQ=255)
cATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCt > 1:448233/1‑139 (MQ=255)
aTCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCAcgcgcg < 2:288499/84‑1 (MQ=255)
aTCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCAcgcgcg > 1:288499/1‑84 (MQ=255)
gCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTg < 2:446441/138‑1 (MQ=255)
aacggaacgCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGAAAAGAt < 2:18757/139‑1 (MQ=255)
gTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTc < 2:196562/107‑1 (MQ=255)
gTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTc > 1:196562/1‑107 (MQ=255)
cctcGCCCCAGGCTTACATCGCTTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGTAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACtt < 1:567040/135‑1 (MQ=255)
cGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTtcatc < 1:416192/139‑1 (MQ=255)
gCCCCAGGCTGACAGCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTtcatca < 2:350296/139‑1 (MQ=255)
aCATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTTCATCAGAACCTTCAcc > 2:5385/1‑139 (MQ=255)
|
TCACGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCTTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTTCATCAGAACCTTCACC > NZ_CP009273/693330‑693592
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTTCAAAACATTCACGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCTTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTTCATCAGAACCTTCAC > NZ_CP009273/693319‑693591
|
CTTCAAAACATTCACGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAGGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGC > SRR3722135.207559/1‑151 (MQ=60)
atgtgtataagagacagGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCA < SRR3722135.210277/134‑1 (MQ=60)
TCACGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAG < SRR3722135.642130/150‑1 (MQ=60)
GGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACAT > SRR3722135.92672/1‑151 (MQ=60)
gaatacacagtgctcggttgttcacattttttttttttttttcaagcagaagacggcatacgagatctagtacggtctcgcgggctcggagatgtgtataagagacagGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGC < SRR3722135.467579/43‑1 (MQ=60)
GTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGC < SRR3722135.460343/151‑1 (MQ=60)
CATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCT > SRR3722135.19006/1‑151 (MQ=60)
CATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCT > SRR3722135.452495/1‑151 (MQ=60)
gagacagGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGC < SRR3722135.569680/144‑1 (MQ=60)
CCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAG < SRR3722135.611960/151‑1 (MQ=60)
GGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTT > SRR3722135.454305/1‑151 (MQ=60)
GGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATctgtctcttatacacatctccgagcccacgagaccgtactagat > SRR3722135.292633/1‑106 (MQ=60)
GAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGctgtctcttatacacatctccg > SRR3722135.199338/1‑129 (MQ=60)
TCCTCGCCCCAGGCTTACATCGCTTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGTAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTTCATCAGAACCT < SRR3722135.574509/150‑1 (MQ=60)
ACGCCCCAGGCTGACATCGCGTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTTCATCAGAACCTTCAC < SRR3722135.421912/151‑1 (MQ=60)
|
CTTCAAAACATTCACGCAGGATGTGTTTTTCCATTTTGCCGTTACCGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCGTGCTTCCACGCCCCAGGCTGACATCGCTTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGTTTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACACTTCATCAGAACCTTCAC > NZ_CP009273/693319‑693591
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
