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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,534,656	C→T	G405R (GGG→AGG)	envZ ←	sensory histidine kinase in two‑component regulatory system with OmpR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,534,656	0	C	T	100.0%	90.9 / NA	29	G405R (GGG→AGG)	envZ	sensory histidine kinase in two‑component regulatory system with OmpR
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (16/13); total (16/13)

TTTTGTCGTGCCCTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCCTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGGCGCGATTCGGC  >  NC_000913/3534525‑3534780

ttttGTCGTGCCCTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATccc                                                                                                                       <  1:468617/139‑1 (MQ=255)

    gTCGTGCCCTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGc                                                                                                                   <  2:603239/139‑1 (MQ=255)

      cGTGCCCTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCg                                                                                                                 <  2:670901/139‑1 (MQ=255)

         gCCCTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTa                                                                                                              >  2:307388/1‑139 (MQ=255)

          cccTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTaa                                                                                                             <  2:529165/139‑1 (MQ=255)

               cgcCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTg                                                                                                        >  2:577488/1‑139 (MQ=255)

               cgcCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTg                                                                                                        >  1:638626/1‑139 (MQ=255)

               cgcCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTg                                                                                                        >  2:1011819/1‑139 (MQ=255)

                       ttACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACt                                                                                                >  2:1064867/1‑139 (MQ=255)

                                  ggCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAACATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGa                                                                                     >  2:836318/1‑139 (MQ=255)

                                     aGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACaa                                                                                  <  1:577488/139‑1 (MQ=255)

                                           gcgcGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCt                                                                            <  2:638626/139‑1 (MQ=255)

                                             gcgAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTgg                                                                          <  1:1064867/139‑1 (MQ=255)

                                                            gccccgcTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACgt                                                           <  1:963078/139‑1 (MQ=255)

                                                                    cgctGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCgg                                                   >  2:601295/1‑139 (MQ=255)

                                                                                 cTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGa                                      >  2:539570/1‑139 (MQ=255)

                                                                                           ccGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCtt                            <  1:307388/139‑1 (MQ=255)

                                                                                                 tGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCg                                                                                                                 >  2:312413/1‑48 (MQ=255)

                                                                                                 tGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCg                                                                                                                 <  1:312413/48‑1 (MQ=255)

                                                                                                     tATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGaa                  >  2:613448/1‑139 (MQ=255)

                                                                                                        ccACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAAc                                                                       >  2:131081/1‑83 (MQ=255)

                                                                                                        ccACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAAc                                                                       <  1:131081/83‑1 (MQ=255)

                                                                                                        ccACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCa               >  1:420419/1‑139 (MQ=255)

                                                                                                             aTACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGgcgc          >  1:674631/1‑139 (MQ=255)

                                                                                                                   tGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGGCGCGAtt      <  1:728360/137‑1 (MQ=255)

                                                                                                                   tGCACAACTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAAGGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGGCGCGAtt      >  2:728360/1‑137 (MQ=255)

                                                                                                                     cacaATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGGCGCGATTCGGc  >  1:709167/1‑139 (MQ=255)

                                                                                                                               aGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGa                                      <  2:79245/93‑1 (MQ=255)

                                                                                                                               aGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGa                                      >  1:79245/1‑93 (MQ=255)

TTTTGTCGTGCCCTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCCTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGGCGCGATTCGGC  >  NC_000913/3534525‑3534780

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A