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
A14 F6 I1 R1	78	2874.5	178397650	99.0%	176613673	98.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AE015451_phaM1	4,741,230	A→G	intergenic (+467/+286)	gltA CDS (citrate synthase) → / ← yeiW CDS (putative oxidoreductase)	–/–

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451_phaM1	4,741,230	0	A	G	90.0%	26.0 / ‑3.9	10	intergenic (+467/+286)	gltA CDS (citrate synthase)/yeiW CDS (putative oxidoreductase)	–/–
Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (6/3); total (6/4)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAC  >  AE015451_phaM1/4741174‑4741351

gCCATGGCGTATTGACCTGGGTATCGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTCCTGCGACTTGCATTCGTGAA‑TCCAGGAACAGGCCCCgg                                                                                  <  6:41012301/99‑2 (MQ=255)

     ggCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTcac                           >  1:186214/1‑149 (MQ=255)

     ggCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTcac                           <  7:89473/149‑1 (MQ=255)

            tGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGa                    >  2:337248/1‑149 (MQ=255)

                  gggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTc                             >  1:216109/1‑134 (MQ=255)

                  gggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTc                             <  2:216109/134‑1 (MQ=255)

                  gggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGcc              <  8:95484/149‑1 (MQ=255)

                      ataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGt          >  2:213041/1‑149 (MQ=255)

                          gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt      >  2:7759/1‑149 (MQ=255)

                              aGCTCTGGTCACATTCGTGCTTGAGCAGCTTCTGCGACTTGC‑ATTCGTGAATCCAGGC‑ACAGGCCCCGNACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAc  >  1:332954/1‑149 (MQ=255)

GCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAC  >  AE015451_phaM1/4741174‑4741351

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A