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
A40 F1 I1 R1	16	59.7	3732628	97.2%	3628114	76.0

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	REL606	1,609,130	A→C	K285Q (AAG→CAG)	insF‑3 →	putative transposase for IS3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	1,609,130	0	A	C	96.4%	107.9 / ‑3.3	28	K285Q (AAG→CAG)	insF‑3	putative transposase for IS3
Reads supporting (aligned to +/- strand): ref base A (1/0); new base C (12/15); total (13/15)
Fisher's exact test for biased strand distribution p-value = 4.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

GGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGCTGT  >  REL606/1609103‑1609201

ggcCTCAGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTc                         <  1:1021756/76‑1 (MQ=14)

ggcCTCAGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTc                         <  1:551686/76‑1 (MQ=14)

  ccTCAGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCAc                       >  1:70100/1‑76 (MQ=21)

  ccTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCAc                       >  1:346769/1‑76 (MQ=35)

    tCAGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCt                     <  1:1113822/76‑1 (MQ=255)

    tCAGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCt                     >  1:1552310/1‑76 (MQ=255)

    tCAGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCt                     >  1:500904/1‑76 (MQ=255)

     cAGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTa                    >  2:1052000/1‑76 (MQ=255)

      aGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTaa                   <  2:392800/76‑1 (MQ=255)

      aGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTaa                   <  1:212853/76‑1 (MQ=255)

      aGTCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTaa                   <  1:62109/76‑1 (MQ=255)

        tCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAAt                 <  2:556304/76‑1 (MQ=255)

        tCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAAt                 >  2:348472/1‑76 (MQ=255)

        tCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAAt                 <  2:271380/76‑1 (MQ=255)

        tCCGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAAt                 <  1:1838916/76‑1 (MQ=255)

         ccGGAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCACATTACGTGGGTAGGATCAATTCACCTAAATa                <  1:907002/76‑1 (MQ=255)

           ggAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACg              >  2:1565506/1‑76 (MQ=255)

           ggAACAATTTGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACg              <  1:101111/76‑1 (MQ=255)

                  tttGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCAtt       <  1:735333/76‑1 (MQ=255)

                   ttGAAAACCAGAACCTCGCTTAGGCCTGTCTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTg      <  2:319551/76‑1 (MQ=255)

                    tGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGc     >  2:244072/1‑76 (MQ=255)

                    tGAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGc     >  1:583954/1‑76 (MQ=255)

                     gAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGCt    >  2:1041965/1‑76 (MQ=255)

                     gAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGCt    <  2:1524044/76‑1 (MQ=255)

                     gAAAACCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGCt    >  1:1451079/1‑76 (MQ=255)

                      aaaaCCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGCTg   <  1:621560/76‑1 (MQ=255)

                       aaaCCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGCTGt  >  2:1423068/1‑76 (MQ=255)

                       aaaCCAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGCTGt  >  2:170091/1‑76 (MQ=255)

GGCCTCAGTCCGGAACAATTTGAAAACAAGAACCTCGCTTAGGCCTGTGTCCATATTACGTGGGTAGGATCAATTCACCTAAATACGAGGCATTGCTGT  >  REL606/1609103‑1609201

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

N/A