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
A31 F30 I1 R1	28	44.1	1499574	99.3%	1489076	139.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,587,586	C→A	intergenic (+155/‑9)	narQ → / → acrD	sensory histidine kinase NarQ/multidrug efflux pump RND permease AcrD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,587,586	0	C	A	100.0%	118.8 / NA	36	intergenic (+155/‑9)	narQ/acrD	sensory histidine kinase NarQ/multidrug efflux pump RND permease AcrD
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (23/13); total (23/13)

CTTAAGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTCCTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACC  >  NC_000913/2587461‑2587716

cTTAAGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCg                                                                                                                      >  2:519719/1‑140 (MQ=255)

  tAAGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGaa                                                                                                                    >  1:383763/1‑140 (MQ=255)

   aaGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAAt                                                                                                                   >  2:152854/1‑140 (MQ=255)

   aaGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAAt                                                                                                                   >  2:602579/1‑140 (MQ=255)

             ataAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTg                                                                                                         >  2:748318/1‑140 (MQ=255)

                 aaGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCg                                                                                                     >  1:394230/1‑140 (MQ=255)

                   gggCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGcc                                                                                                   <  2:289922/140‑1 (MQ=255)

                      cATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCa                                                                                                >  1:286956/1‑140 (MQ=255)

                      cATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCa                                                                                                >  2:683490/1‑140 (MQ=255)

                      cATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCa                                                                                                >  1:197807/1‑140 (MQ=255)

                                   aTTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGt                                                                                   >  1:412366/1‑140 (MQ=255)

                                     tAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGATACAGTGAACCAAGTCAAGCCTACAACGTTACGCAGAAAAACGAGGGACTCTTTTAATGGCGAATTTCTTTATTGATCCCCCCATTTTTGCCAgggatt                                                                                 >  2:353696/1‑137 (MQ=255)

                                     aaaCTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGc                                                                                 >  1:622780/2‑140 (MQ=255)

                                       aCTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTg                                                                               >  1:378460/1‑140 (MQ=255)

                                         tCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGc                                                                             >  1:579145/1‑140 (MQ=255)

                                           cTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCaa                                                                           <  1:602579/140‑1 (MQ=255)

                                             ttttttCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATc                                                                         <  2:246707/140‑1 (MQ=255)

                                                      cACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTgtgt                                                                <  2:197807/140‑1 (MQ=255)

                                                           ttGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGAc                                                           <  2:734294/140‑1 (MQ=255)

                                                              gCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAgg                                                        >  1:196181/1‑140 (MQ=255)

                                                                   tACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTAccc                                                   >  1:170342/1‑140 (MQ=255)

                                                                   tACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTAccc                                                   >  1:609479/1‑140 (MQ=255)

                                                                      cTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTgg                                                <  2:378460/140‑1 (MQ=255)

                                                                      cTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTgg                                                <  2:622780/140‑1 (MQ=255)

                                                                         gCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGa                                             >  1:97652/1‑140 (MQ=255)

                                                                         gCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGa                                             >  1:91564/1‑140 (MQ=255)

                                                                                   tGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCAtt                                   <  1:707097/140‑1 (MQ=255)

                                                                                          aGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGtt                            <  1:480087/140‑1 (MQ=255)

                                                                                          aGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGtt                            <  1:467320/140‑1 (MQ=255)

                                                                                          aGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGtt                            >  1:105143/1‑140 (MQ=255)

                                                                                           gTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTg                           <  2:609479/140‑1 (MQ=255)

                                                                                                     cAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATAccc                 >  1:21339/1‑140 (MQ=255)

                                                                                                          aTACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGAtc            >  2:260591/1‑140 (MQ=255)

                                                                                                           tACGCAGAAACACGAGGTACTCTTTTAATGACGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGAtct           >  1:664328/1‑140 (MQ=255)

                                                                                                                aGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCgcgc      >  2:389817/1‑140 (MQ=255)

                                                                                                                    acacGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCAcc  <  2:269566/140‑1 (MQ=255)

                                                                                                                    acacGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCAcc  <  2:286956/140‑1 (MQ=255)

CTTAAGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTCCTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACC  >  NC_000913/2587461‑2587716

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