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
A12 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,619,119	T→A	intergenic (+130/‑73)	nikR → / → rhsB	DNA‑binding transcriptional repressor NikR/rhs element protein RhsB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,619,119	0	T	A	100.0%	163.0 / NA	46	intergenic (+130/‑73)	nikR/rhsB	DNA‑binding transcriptional repressor NikR/rhs element protein RhsB
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (28/18); total (28/18)

TGGGTCCTTTGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCATTGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCA  >  NC_000913/3618999‑3619253

tGGGTCCTTTGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTttct                                                                                                                     <  2:443745/140‑1 (MQ=255)

    tCCTTTGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGc                                                                                                                 >  1:419668/1‑140 (MQ=255)

      cTTTGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTTCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCtt                                                                                                               >  1:681652/1‑140 (MQ=255)

      cTTTGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGAcc                                                                                                                                 >  2:393545/1‑122 (MQ=255)

      cTTTGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGAcc                                                                                                                                 <  1:393545/122‑1 (MQ=255)

      cTTTGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCtt                                                                                                               >  1:153972/1‑140 (MQ=255)

         tGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCttttt                                                                                                            >  2:70355/1‑140 (MQ=255)

              aaCGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTAt                                                                                                       <  1:70355/140‑1 (MQ=255)

                cGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTAGCTTTTTCGTATGa                                                                                                     >  1:804527/1‑140 (MQ=255)

                     aacaaAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATa                                                                                                >  2:769880/1‑140 (MQ=255)

                      acaaAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATAc                                                                                               <  2:447362/140‑1 (MQ=255)

                             gCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCg                                                                                                          <  2:746881/122‑1 (MQ=255)

                             gCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCg                                                                                                          >  1:746881/1‑122 (MQ=255)

                             gCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCAtt                                                                                        >  2:7281/1‑140 (MQ=255)

                             gCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCAtt                                                                                        >  1:760729/1‑140 (MQ=255)

                                          cTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGaaa                                                                           >  2:834556/1‑140 (MQ=255)

                                          cTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGaaa                                                                           >  2:205158/1‑140 (MQ=255)

                                           tGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGaaaa                                                                          <  1:205158/140‑1 (MQ=255)

                                           tGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGaaaa                                                                          <  1:834556/140‑1 (MQ=255)

                                           tGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGaaaa                                                                          <  2:153972/140‑1 (MQ=255)

                                               tCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGAt                                                                      >  2:170268/1‑140 (MQ=255)

                                                    tctAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTAc                                                                 >  1:245391/1‑140 (MQ=255)

                                                             ccTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCgg                                                        >  1:119691/1‑140 (MQ=255)

                                                             ccTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCgg                                                        >  1:683927/1‑140 (MQ=255)

                                                              cTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGa                                                       >  1:760364/1‑140 (MQ=255)

                                                               tATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGaa                                                      >  1:200449/1‑140 (MQ=255)

                                                                aTCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGC‑TTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGaaaa                                                    >  2:633021/1‑140 (MQ=255)

                                                                 tCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGaaaa                                                    >  2:381347/1‑140 (MQ=255)

                                                                     aaCCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACcgg                                                >  2:48042/1‑140 (MQ=255)

                                                                      aCCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACcggc                                               >  1:505760/1‑140 (MQ=255)

                                                                      aCCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACcggc                                               >  1:314573/1‑140 (MQ=255)

                                                                        cTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTAGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACcggcgg                                             <  2:804527/140‑1 (MQ=255)

                                                                                          cTAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGa                           <  2:760364/140‑1 (MQ=255)

                                                                                           tAAATATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGAc                          <  2:760729/140‑1 (MQ=255)

                                                                                            aaaTATATTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACg                         <  1:48042/140‑1 (MQ=255)

                                                                                                atatTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGt                     <  2:505760/140‑1 (MQ=255)

                                                                                                  atTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTAt                   >  2:244485/1‑140 (MQ=255)

                                                                                                  atTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTAt                   >  2:550768/1‑140 (MQ=255)

                                                                                                  atTCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTAt                   >  1:314595/1‑140 (MQ=255)

                                                                                                    tCCTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATgg                 >  1:879881/1‑140 (MQ=255)

                                                                                                     ccTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTAt                   >  2:711512/1‑137 (MQ=255)

                                                                                                     ccTAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTAt                   <  1:711512/137‑1 (MQ=255)

                                                                                                       tAAAAATCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCgg              <  1:244485/140‑1 (MQ=255)

                                                                                                            aTCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTATGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCa         <  1:170268/140‑1 (MQ=255)

                                                                                                            aTCTTCAATTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCa         <  2:879881/140‑1 (MQ=255)

                                                                                                               ttcaattcaaTGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTg      >  1:646306/1‑140 (MQ=255)

                                                                                                                   aTTCAATGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCa  <  2:683927/140‑1 (MQ=255)

TGGGTCCTTTGGTGAACGATCAACAAAGGGCCACTAGCACACCTGATTCCTCTCTAAATACCCTATCCGAACCTTCTCTTTTGTAACGTTCTAAATATATTCCTAAAAATCTTCAATTCATTGTGACCACAAGTTTTTCTTCGCTTTTTCGTATGAAGATACTGTCATTAAAATAATAGAAAAGGATTTTACGATGAGCGGAAAACCGGCGGCGCGTCAGGGTGACATGACGCAGTATGGCGGTAGCATTGTTCA  >  NC_000913/3618999‑3619253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A