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 |
|
A4 F18 I1 R1
|
54 |
68.8 |
3145800 |
98.6% |
3101758 |
145.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
5,558,423 |
+GCC |
intergenic (‑84/+87) |
PP_4887 ← / ← PP_4888 |
hypothetical protein/methyl‑accepting chemotaxis transducer |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 5,558,423 | 1 | . | G | 92.9%
| 23.6
/ ‑2.8
| 14 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base G (4/9); minor base C (0/1); total (4/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-01 |
| * | NC_002947_CJ‑RC | 5,558,423 | 2 | . | C | 100.0%
| 44.3
/ NA
| 14 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (4/10); total (4/10) |
| * | NC_002947_CJ‑RC | 5,558,423 | 3 | . | C | 92.9%
| 40.9
/ ‑2.8
| 14 | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (4/9); total (4/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01 |
TGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGC‑G‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558279‑5558551
|||
tGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgc‑ggccc > 7:385410/1‑145 (MQ=255)
aGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTAt < 8:385410/148‑1 (MQ=255)
ggTCGGCGGGGGCTGCGATTAGTGGGGCGGAAATGAGCAACTCCTTTTGTCTTGGGCCGCCTACAGCATCTAAACCGCGATCAGGTGTGGGTGGGGCGTTGTGTCGCTAACGGGCCGCTTAGC‑GGCCCCGGCAATTTCCGCGTGTATGc < 4:88182/149‑1 (MQ=255)
ttAGTCGGGTGGACATGTGCAACTCTTTTTGTCATGTGTCGCGGACAGCATAGCAACACCGGTCTGGTGTGGGAGCGGCCTTGTGTCGCTAAAGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 6:365191/148‑1 (MQ=37)
ttAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGCAGCC‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgct < 2:151482/149‑1 (MQ=38)
tgtgTCGGGCTGAAATCACCAACTCTTTTTGTCTTGTGTCGCCTACATAATAGCACCCCCGCTCTGGTGTGGGAGCGGCTTTGTGTCGCTAACGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGgctgc < 4:297069/145‑1 (MQ=255)
gccGGCCGCACATGACCAACTCCTTTTGCCATGGGCCGCCGACAGCATCCCAACACCGCTCAGGTGGGGGCGCGCCCTTGTGCCGCCAACGGCCCGCATCGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTAt < 2:379787/146‑1 (MQ=255)
tCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTaga > 3:297069/1‑146 (MQ=38)
aCATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACCCCGCGCCGGTGGGGGAGCGGCCTTGTGTCGCGAACGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCATAGCAGccccag < 8:146183/149‑4 (MQ=25)
tGAGAAACTCCTTTTGACCTGTGGCCCCGACTGCATACCAACCCCGCTCTGGTGTGGGTGCGGCCTTGGGGCCCGAATGGGCCGCATCGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTcgc < 7:288635/149‑1 (MQ=255)
ttttGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgc‑g > 3:376512/1‑80 (MQ=255)
ttttGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAgc‑g < 4:376512/80‑1 (MQ=255)
gCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGc > 7:86171/1‑91 (MQ=21)
gggcggtgtgCCGCTAACGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGAACAAAACCTGGGGCTGCTATGCAGCCCTTTCGCTACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGgcgc < 2:91444/143‑1 (MQ=255)
ccTTGTGTCGCTAAAGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCa < 2:124508/149‑1 (MQ=38)
gcgAAAGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTg > 7:12420/1‑133 (MQ=38)
gAAAGGGCCGCATAGC‑GGCCCCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAgccgc > 5:338879/1‑148 (MQ=255)
|||
TGTCACTGTGCAGGAAATTCAGGTCGGCCTGGGCAGCGATTAGTCGGGCGGACATGAGCAACTCCTTTTGTCATGTGTCGCCGACAGCATAGCAACACCGCTCAGGTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCCGCATAGC‑G‑‑‑CCGGCAATTTCCGCGTGTATGCAACAAACCTGGGGCTGCTATGCAGCCCTTTCGCGACACAAGGCCCACAAAGGACCGCGCAGGCTTCAGGCCCGGAACTGGCCCAGGCTGGCGCGCAGCTGAGCCGC > NC_002947_CJ‑RC/5558279‑5558551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
