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 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

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%	91.8 / 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 (14/15); total (14/15)

CCCTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCCTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGGCGCGATTCGGCTCCGT  >  NC_000913/3534535‑3534785

cccTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTaa                                                                                                                  <  2:238269/139‑1 (MQ=255)

 ccTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAAt                                                                                                                 <  2:155437/139‑1 (MQ=255)

                     aCTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGt                                                                                                                          <  1:178414/110‑1 (MQ=255)

                     aCTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGt                                                                                                                          >  2:178414/1‑110 (MQ=255)

                        ggCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGa                                                                                          >  2:243675/1‑139 (MQ=255)

                           aGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACaa                                                                                       <  2:795119/139‑1 (MQ=255)

                                 gtgcgAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACg                                                                                    >  1:180698/3‑136 (MQ=255)

                                 gtgcgAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACg                                                                                    <  2:180698/134‑1 (MQ=255)

                                 gcgcGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCt                                                                                 >  1:467303/1‑139 (MQ=255)

                                      aaTGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAAc                                                                            <  2:888454/139‑1 (MQ=255)

                                            aaGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGc                                                                      <  1:129781/139‑1 (MQ=255)

                                             aGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCt                                                                     <  1:243675/139‑1 (MQ=255)

                                                  gccccgcTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACgt                                                                <  2:467303/139‑1 (MQ=255)

                                                        ctcgctGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAAc                                                                            <  2:763659/121‑1 (MQ=255)

                                                        ctcgctGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAAc                                                                            >  1:763659/1‑121 (MQ=255)

                                                         tcgctGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCg                                                         >  1:375122/1‑139 (MQ=255)

                                                                  ccAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACaa                                                                                       >  1:536647/1‑100 (MQ=255)

                                                                  ccAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACaa                                                                                       <  2:536647/100‑1 (MQ=255)

                                                                                 ccGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCtt                                 <  1:138844/139‑1 (MQ=255)

                                                                                  cGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTc                                <  2:375122/139‑1 (MQ=255)

                                                                                  cGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTc                                >  2:127586/1‑139 (MQ=255)

                                                                                          ttATCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGa                        >  2:682771/1‑139 (MQ=255)

                                                                                            aTCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAAc                      >  2:288419/1‑139 (MQ=255)

                                                                                             tCCACGATACGCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAAcc                     >  1:753793/1‑139 (MQ=255)

                                                                                                       gCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACaa                                                                                       <  2:886928/63‑1 (MQ=255)

                                                                                                       gCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACaa                                                                                       >  1:886928/1‑63 (MQ=255)

                                                                                                       gCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGgcg                >  2:49518/1‑134 (MQ=255)

                                                                                                       gCTGCACAATTGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGgcg                <  1:49518/134‑1 (MQ=255)

                                                                                                                ttGCCAGCCTTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGGCGCGATTCGGCTCCGt  >  2:599030/1‑139 (MQ=255)

CCCTGCGCCCGCGTTACCGGCACTGGCAGCCAGGCGCGAATGGAAAGCCCGCCCCGCTCGCTGGTGCCAAGCTCCAGCATCCCGTTATGGTTATCCACGATACGCTGCACAATTGCCAGCCCTAATCCCGTGCCGCTAATGGTGCGCGCACTGTCGCCGCGGACAAACGGCTGGAACAGGTGCTTACGTTGTTCCGGCGCAATTCCCGGACCGTCATCTTCCACCTGGAACCAGGCGCGATTCGGCTCCGT  >  NC_000913/3534535‑3534785

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A