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 F50 I2 R1	104	44.1	1376607	98.9%	1361464	150.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,590,692	T→C	T74A (ACG→GCG)	ugpA ←	sn‑glycerol‑3‑phosphate ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,590,692	0	T	C	97.1%	121.0 / ‑3.7	34	T74A (ACG→GCG)	ugpA	sn‑glycerol‑3‑phosphate ABC transporter permease
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (17/16); total (18/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

GAGCCACGGCGTAAGGCAGCAACATTAAGGTTTGATAGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGTCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGCCAGATAAAAAAGATAACGG  >  NC_000913/3590557‑3590838

gAGCCACGGCGTAAGGCAGCAACATTAAGGTTTGATAGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCgag                                                                                                                                     <  2:684645/151‑1 (MQ=255)

gAGCCACGGCGTAAGGCAGCAACATTAAGGTTTGATAGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCgag                                                                                                                                     <  2:53292/151‑1 (MQ=255)

   ccACGGCGTAAGGCAGCAACATTAAGGTTTGATAGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGAta                                                                                                                                  <  2:138630/151‑1 (MQ=255)

          gTAAGGCAGCAACATTAAGGTTTGATAGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTg                                                                                                                           <  1:532153/151‑1 (MQ=255)

            aaGGCAGCAACATTAAGGTTTGATAGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGCGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTc                                                                                                                         >  2:493082/1‑151 (MQ=255)

                                 gATAGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGtt                                                                                                    <  1:245465/151‑1 (MQ=255)

                                    aGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATc                                                                                                 >  1:398479/1‑151 (MQ=255)

                                      aaaCGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATcc                                                                                                >  1:454628/1‑150 (MQ=255)

                                           gCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGAC‑AAGGTGCTGAATTTTATCGTCGCCCCGAAGGAGTCGAGGTAGTAGCTGTCATGGAACAGCGTGACGCAGTTATCCAGGCCg                                                                                          >  1:464082/1‑150 (MQ=255)

                                               ccGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACa                                                                                       >  2:686179/1‑150 (MQ=255)

                                               ccGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACa                                                                                       >  2:177045/1‑150 (MQ=255)

                                                   gcACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAActg                                                                                  >  2:647683/1‑151 (MQ=255)

                                                      cGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGGGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAActggct                                                                               >  1:179080/1‑151 (MQ=255)

                                                          gTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGgag                                                                           <  1:271581/151‑1 (MQ=255)

                                                            aCTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGgaga                                                                          <  2:181363/150‑1 (MQ=255)

                                                            aCTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGaa                                                                         <  2:241054/151‑1 (MQ=255)

                                                                caccaGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCa                                                                     <  2:483221/151‑1 (MQ=255)

                                                                       gccgcAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGAt                                                              <  2:40908/151‑1 (MQ=255)

                                                                            aaaGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACg                                                         <  2:341231/151‑1 (MQ=255)

                                                                                   aGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTa                                                  <  1:277911/151‑1 (MQ=255)

                                                                                     cGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGc                                                >  2:381481/1‑151 (MQ=255)

                                                                                       aTACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGTCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCg                                               >  1:645719/1‑150 (MQ=255)

                                                                                           cAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTAc                                          <  1:511972/151‑1 (MQ=255)

                                                                                              cAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACcac                                       <  1:523202/151‑1 (MQ=255)

                                                                                                 aCCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAAc                                    >  1:160630/1‑151 (MQ=255)

                                                                                                       gACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCg                              <  1:300419/151‑1 (MQ=255)

                                                                                                       gACGGTGACAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCg                              >  1:32931/1‑151 (MQ=255)

                                                                                                               cAAAGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAgg                      >  2:638617/1‑151 (MQ=255)

                                                                                                                aaaGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGc                     >  1:279452/1‑151 (MQ=255)

                                                                                                                  aGGTGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGcc                    >  1:383386/1‑150 (MQ=255)

                                                                                                                     tGCTGAATTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGcc                    >  1:447969/1‑147 (MQ=255)

                                                                                                                           aTTTTATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGCCAGATaaaaaa          <  1:41333/151‑1 (MQ=255)

                                                                                                                               tATCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGCCAGATAAAAAAGAt       >  2:262270/1‑150 (MQ=255)

                                                                                                                                aTCGTCGCCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGCCAGATAAAAAAGATa      >  1:181864/1‑150 (MQ=255)

                                                                                                                                  cgtcgcCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGCCAGATAAAAAAGATAACg   >  2:186899/1‑151 (MQ=255)

                                                                                                                                   gtcgccCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGCCAGATAAAAAAGATAACgg  >  1:353701/1‑151 (MQ=255)

GAGCCACGGCGTAAGGCAGCAACATTAAGGTTTGATAGAAACGGCTGCCGCGCACGATGTACTCCACCAGCGCCGCAAAGAACAGCGATACCAGCAAACCGCTGACGGTGACAAAGGTGCTGAATTTTATCGTCGTCCAGAAGGAGTCGAGATAGTAGCTGTCATGGAACAGCGTGACGAAGTTATCCAGGCCGACAAACTGGCTGGAGAAACCAAACGGATCGACGCTTTGTAGCGAGTACCACAACGCTTCGCCCGCAGGCCAGATAAAAAAGATAACGG  >  NC_000913/3590557‑3590838

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A