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
A2 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,271,455	G→A	T132I (ACC→ATC)	chaA ←	calcium/sodium:proton antiporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,271,455	0	G	A	100.0%	132.2 / NA	42	T132I (ACC→ATC)	chaA	calcium/sodium:proton antiporter
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (19/23); total (19/23)

CAGTAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGGTGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAC  >  NC_000913/1271331‑1271590

cAGTAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGa                                                                                                                           <  1:709710/139‑1 (MQ=255)

      cGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGccc                                                                                                                     <  2:637421/139‑1 (MQ=255)

         cTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATATCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCcaac                                                                                                                  >  1:712292/1‑139 (MQ=255)

           gACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCcaacaa                                                                                                                >  1:215307/1‑139 (MQ=255)

            aCCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACaat                                                                                                               >  2:474495/1‑139 (MQ=255)

                             ccgcAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAg                                                                                              <  1:448561/139‑1 (MQ=255)

                                caggcagAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAACACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGccc                                                                                           <  1:438223/139‑1 (MQ=255)

                                      gagCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGt                                                                                     <  1:474495/139‑1 (MQ=255)

                                      gagCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGt                                                                                     <  2:821167/139‑1 (MQ=255)

                                      gagCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGt                                                                                     <  1:406521/139‑1 (MQ=255)

                                             tGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGc                                                                                                                                     >  2:375577/1‑84 (MQ=255)

                                             tGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGc                                                                                                                                     <  1:375577/84‑1 (MQ=255)

                                                 aaTACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATaa                                                                          <  2:712292/139‑1 (MQ=255)

                                                    aCCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCa                                                                                          >  2:831965/1‑120 (MQ=255)

                                                    aCCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCa                                                                                          <  1:831965/120‑1 (MQ=255)

                                                    aCCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGa                                                                       <  2:65273/139‑1 (MQ=255)

                                                       aGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTg                                                                    >  2:67790/1‑139 (MQ=255)

                                                         tACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAAc                                                                                                 >  1:841763/1‑108 (MQ=255)

                                                         tACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAAc                                                                                                 <  2:841763/108‑1 (MQ=255)

                                                                aTCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCAt                                                                            >  1:34366/1‑122 (MQ=255)

                                                                aTCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCAt                                                                            <  2:34366/122‑1 (MQ=255)

                                                                aTCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCg                                                           <  1:67790/139‑1 (MQ=255)

                                                                     cAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCa                                                      <  2:215307/139‑1 (MQ=255)

                                                                           gAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCa                                                      <  2:689330/133‑1 (MQ=255)

                                                                           gAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCa                                                      >  1:689330/1‑133 (MQ=255)

                                                                                  gcAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTg                                         >  2:469011/1‑139 (MQ=255)

                                                                                        aaaTACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGccc                                                                                                                     <  2:320267/57‑1 (MQ=255)

                                                                                        aaaTACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGccc                                                                                                                     >  1:320267/1‑57 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGAc                                                                                                                          <  2:976669/44‑1 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGAc                                                                                                                          >  1:976669/1‑44 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGcc                                                                                                                      <  1:974973/48‑1 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGcc                                                                                                                      >  2:974973/1‑48 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGcc                                                                                                    <  2:795211/66‑1 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGcc                                                                                                    >  1:795211/1‑66 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTAt                                                        >  2:330817/1‑110 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTAt                                                        <  1:330817/110‑1 (MQ=255)

                                                                                                cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCg                           >  1:923330/1‑139 (MQ=255)

                                                                                                   gATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATaga                                                              >  1:968035/1‑101 (MQ=255)

                                                                                                   gATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATaga                                                              <  2:968035/101‑1 (MQ=255)

                                                                                                      aCCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGt                         <  2:469791/135‑1 (MQ=255)

                                                                                                      aCCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGt                         >  1:469791/1‑135 (MQ=255)

                                                                                                                         tGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAc  >  1:448934/1‑139 (MQ=255)

CAGTAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGGTGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAC  >  NC_000913/1271331‑1271590

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A