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
A10 F28 I1 R1	126	51.4	1736588	99.0%	1719222	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,319,449	T→C	N143S (AAC→AGC)	rcsC ←	sensory histidine kinase RcsC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,319,449	0	T	C	100.0%	158.3 / NA	46	N143S (AAC→AGC)	rcsC	sensory histidine kinase RcsC
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (25/21); total (25/21)

ATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGTTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAGGC  >  NC_000913/2319313‑2319580

atcatcTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTa                                                                                                                                  >  2:468512/1‑140 (MQ=255)

           gtgCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGcc                                                                                                                       >  2:126579/1‑140 (MQ=255)

           gtgCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGcc                                                                                                                       >  2:92830/1‑140 (MQ=255)

              cATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCa                                                                                                                    >  1:227583/1‑140 (MQ=255)

                        tttattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTAt                                                                                                          >  1:689475/1‑140 (MQ=255)

                          tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATcg                                                                                                        <  1:126579/140‑1 (MQ=255)

                          tattGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATcg                                                                                                        >  1:49935/1‑140 (MQ=255)

                           attGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATcgc                                                                                                       >  2:458536/1‑140 (MQ=255)

                             tGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCgcgc                                                                                                     <  1:468512/140‑1 (MQ=255)

                               aTGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCa                                                                                                   >  2:520332/1‑140 (MQ=255)

                                 gCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGt                                                                                                 <  2:227583/140‑1 (MQ=255)

                                  cGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTa                                                                                                >  2:308022/1‑140 (MQ=255)

                                  cGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTa                                                                                                >  1:74846/1‑140 (MQ=255)

                                    ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCTGCAGAAAAATTATCGCGCCAGTAgc                                                                                              >  1:712873/1‑140 (MQ=255)

                                    ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCgcgc                                                                                                     >  2:579275/1‑133 (MQ=255)

                                    ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCgcgc                                                                                                     <  1:579275/133‑1 (MQ=255)

                                    ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAgc                                                                                              >  2:404862/1‑140 (MQ=255)

                                    ttCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAgc                                                                                              >  1:855221/1‑140 (MQ=255)

                                         gCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATa                                                                                         >  2:504544/1‑140 (MQ=255)

                                           aaaGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATaaa                                                                                       <  1:92830/140‑1 (MQ=255)

                                             aGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAAcc                                                                                     >  2:686726/1‑140 (MQ=255)

                                              gCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCa                                                                                    <  1:236198/140‑1 (MQ=255)

                                                 ttCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGc                                                                                 >  2:314198/1‑140 (MQ=255)

                                                     aCGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAAt                                                                             <  1:308022/140‑1 (MQ=255)

                                                     aCGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAAt                                                                             <  1:520332/140‑1 (MQ=255)

                                                       gcgGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGa                                                                           <  2:398262/140‑1 (MQ=255)

                                                         ggTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACt                                                                         >  2:530544/1‑140 (MQ=255)

                                                                  ttCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAAc                                                                <  1:785850/140‑1 (MQ=255)

                                                                  ttCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAAc                                                                >  1:655624/1‑140 (MQ=255)

                                                                     cACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTc                                                             >  2:190951/1‑140 (MQ=255)

                                                                       cTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGc                                                           <  2:74846/140‑1 (MQ=255)

                                                                        tGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGcc                                                          <  2:391775/140‑1 (MQ=255)

                                                                           cATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAgg                                                       >  2:191735/1‑140 (MQ=255)

                                                                                  cGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACt                                                <  1:686726/140‑1 (MQ=255)

                                                                                  cGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACt                                                <  2:855221/140‑1 (MQ=255)

                                                                                       aCCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTg                                           >  2:54924/1‑140 (MQ=255)

                                                                                       aCCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTg                                           >  2:578157/1‑140 (MQ=255)

                                                                                          gAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCgg                                        <  1:458536/140‑1 (MQ=255)

                                                                                                 gCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATc                                 >  2:744456/1‑140 (MQ=255)

                                                                                                   cATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCgg                               >  1:367286/1‑140 (MQ=255)

                                                                                                     tGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAg                             <  1:803289/140‑1 (MQ=255)

                                                                                                           ggTTATCGCTGCCGATTAAAAATCCCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCa                       <  1:431503/140‑1 (MQ=255)

                                                                                                                       cGATTAAAAATACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCa           <  2:712873/140‑1 (MQ=255)

                                                                                                                              aaaTACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAg    <  1:404862/140‑1 (MQ=255)

                                                                                                                              aaaTACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAg    <  1:190951/140‑1 (MQ=255)

                                                                                                                                aTACCCGGCTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAGGc  <  1:715878/140‑1 (MQ=255)

ATCATCTTGTGGTGCATTTCGATATTTATTGATGCGTTCATGCAAAGCTTTCAACGCGGTATCGCGTTCCACTGGCATATCACGCAGACCGAAATTGGCCATGCAGAGGTTATCGCTGCCGATTAAAAATACCCGGTTTAGATCGTAAGCCGCAGAAAAATTATCGCGCCAGTAGCGCATAAACCACGCCAATGACTCCAGAGAACCTCGCCAGGTGTTACTCATTGCGGAACAATCGGAGTCGGCAAACAGCGGTTCAAACGCAGGC  >  NC_000913/2319313‑2319580

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A