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 |
|
A0 F0 I1 R1
|
61 |
39.0 |
4165548 |
97.4% |
4057243 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,477,291 |
+GC |
pseudogene (63/1363 nt) |
tdcG ← |
L‑serine ammonia‑lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,477,291 | 1 | . | G | 100.0%
| 80.7
/ NA
| 23 | pseudogene (63/1363 nt) | tdcG | L‑serine ammonia‑lyase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (15/8); total (15/8) |
| * | NC_017635 | 3,477,291 | 2 | . | C | 100.0%
| 79.6
/ NA
| 23 | pseudogene (63/1363 nt) | tdcG | L‑serine ammonia‑lyase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (15/8); total (15/8) |
TAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑CCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTT > NC_017635/3477242‑3477329
||
taaGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTg > 1:1253007/1‑50 (MQ=255)
aaGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTgg > 2:1437638/1‑49 (MQ=255)
aaGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTgg > 2:1396032/1‑49 (MQ=255)
aaGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTgg > 2:585709/1‑49 (MQ=255)
aGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTgtc > 2:202320/1‑48 (MQ=255)
aGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTggc > 2:1091539/1‑48 (MQ=255)
aGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTgg < 2:1719112/49‑2 (MQ=255)
gCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑gcc < 2:321881/50‑1 (MQ=255)
cAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGc < 2:1719178/49‑1 (MQ=37)
aGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCg > 1:695189/1‑49 (MQ=37)
gCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGaa > 2:639693/1‑50 (MQ=38)
gCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGaa > 1:1791384/1‑50 (MQ=38)
gCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGaa > 2:1356357/1‑50 (MQ=38)
gATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 2:803421/1‑50 (MQ=38)
aTCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTg > 1:994474/1‑49 (MQ=37)
cAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAg > 2:1304935/1‑50 (MQ=38)
aaTAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAgg > 1:486401/1‑50 (MQ=38)
aaTAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAgg < 2:1466548/50‑1 (MQ=38)
aaTAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAgg > 2:1359587/1‑50 (MQ=38)
aaTAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAgg < 1:1321801/50‑1 (MQ=38)
aaTAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAg < 1:1239531/49‑1 (MQ=37)
aTAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAggg < 1:742683/50‑1 (MQ=38)
aTAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAgg > 1:241064/1‑49 (MQ=37)
aTAAAACTTTTTCCGGCATACATTGGCCCCACGGTATGCGAACTGGAgg > 1:98116/1‑49 (MQ=255)
aaaaCTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGAc > 2:1196759/1‑50 (MQ=38)
aCTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCaa < 1:921540/50‑1 (MQ=25)
tCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCa < 2:1930696/49‑1 (MQ=21)
cGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAAt < 1:634359/49‑1 (MQ=21)
ggCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAAttt > 1:2062968/1‑50 (MQ=25)
cattcattGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAAtttt > 2:1919/1‑49 (MQ=21)
cattcattGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAAtttt > 1:1056154/1‑49 (MQ=21)
||
TAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑CCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTT > NC_017635/3477242‑3477329
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ 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
TAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑CCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAATATCGA > NC_017635/3477242‑3477340
|
TAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑G > M01420:85:000000000‑AC936:1:2103:18290:28448/1‑51 (MQ=60)
TACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGG > M01420:85:000000000‑AC936:1:1102:3989:19988/1‑51 (MQ=60)
TACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGG > M01420:85:000000000‑AC936:1:2112:8182:17351/1‑51 (MQ=60)
CTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGT > M01420:85:000000000‑AC936:1:1109:13715:13702/1‑50 (MQ=60)
AGCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGA > M01420:85:000000000‑AC936:1:1110:23143:13128/1‑50 (MQ=60)
GCCGATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAAC > M01420:85:000000000‑AC936:1:2111:16335:8861/1‑51 (MQ=60)
ATCAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGG > M01420:85:000000000‑AC936:1:1114:1769:14667/1‑50 (MQ=60)
CAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGG < M01420:85:000000000‑AC936:1:2104:18943:25401/51‑1 (MQ=60)
CAATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAG < M01420:85:000000000‑AC936:1:2103:5849:22363/50‑1 (MQ=60)
AATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGG < M01420:85:000000000‑AC936:1:1111:14815:4082/51‑1 (MQ=60)
AATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGG > M01420:85:000000000‑AC936:1:1107:16787:16389/1‑51 (MQ=60)
ATAAAACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGG > M01420:85:000000000‑AC936:1:1104:21615:9599/1‑50 (MQ=60)
ATAAAACTTTTTCCGGCATACATTGGCCCCACGGTATGCGAACTGGAGGG > M01420:85:000000000‑AC936:1:1102:11626:11358/1‑50 (MQ=44)
AACTTTTTCCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAA < M01420:85:000000000‑AC936:1:1113:6388:14960/51‑1 (MQ=60)
CCGGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAAT < M01420:85:000000000‑AC936:1:1109:16797:16814/50‑1 (MQ=60)
GGCATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTT > M01420:85:000000000‑AC936:1:2114:4334:20850/1‑51 (MQ=60)
CATTCATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTG > M01420:85:000000000‑AC936:1:2101:14442:11151/1‑50 (MQ=60)
CATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT < M01420:85:000000000‑AC936:1:2111:19864:5079/51‑1 (MQ=60)
ATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > M01420:85:000000000‑AC936:1:1113:16687:6810/1‑50 (MQ=60)
ATTGGCCCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAAT > M01420:85:000000000‑AC936:1:2112:5654:9309/1‑50 (MQ=60)
C‑‑CCCACGGAATGCGAACTGGAGGGACCAATCCCAATTTTGAAAATATCGA > M01420:85:000000000‑AC936:1:2114:23441:6691/1‑50 (MQ=60)
|
TAAGCCGCTACTTTCCAGCCGATCAATAAAACTTTTTCCGGCATTCATTG‑‑CCCACGGTATGCGAACTGGAGGGACCAATCCCAATTTTGAAAATATCGA > NC_017635/3477242‑3477340
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
