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 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,673,117	C→T	W11* (TGG→TGA)	mdtI ←	multidrug efflux system transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,673,117	0	C	T	100.0%	31.1 / NA	12	W11* (TGG→TGA)	mdtI	multidrug efflux system transporter
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (4/8); total (4/8)

ACGGCTTGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGCCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCGGCGACCA  >  NC_000913/1672983‑1673218

aCGGCTTGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAgg                                                                                                   <  2:505458/139‑1 (MQ=255)

      tGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGTAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGt                                                                                             >  2:664966/1‑139 (MQ=255)

         gaAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGTGAGAGCAAGCCAAATATCTTTCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGaa                                                                                          <  2:401124/139‑1 (MQ=255)

         gaAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGaa                                                                                          <  1:752599/139‑1 (MQ=255)

                                             gagaGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCa                                                      <  1:664966/139‑1 (MQ=255)

                                                agCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGaa                                                                                          >  1:29198/1‑100 (MQ=255)

                                                agCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGaa                                                                                          <  2:29198/100‑1 (MQ=255)

                                                  cAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTc                                                                  <  1:234065/122‑1 (MQ=255)

                                                  cAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTc                                                                  >  2:234065/1‑122 (MQ=255)

                                                                                                 cGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCGGCGACCa  <  1:557619/139‑1 (MQ=255)

                                                                                                                         ttGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTc                                                             <  1:895298/56‑1 (MQ=255)

                                                                                                                         ttGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTc                                                             >  2:895298/1‑56 (MQ=255)

ACGGCTTGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGCCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCGGCGACCA  >  NC_000913/1672983‑1673218

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A