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 F1 I1 R1	760	58.2	3022526	90.8%	2744453	102.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,849,792	(C)_5→4	coding (345/1503 nt)	uhpB ←	sensory histidine kinase in two‑component regulatory sytem with UhpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,849,788	0	C	.	100.0%	161.4 / NA	40	coding (349/1503 nt)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (19/21); total (19/21)

CGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCGCCCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGC  >  NC_000913/3849650‑3849908

cGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                          <  2:1327197/139‑1 (MQ=255)

 gagaTAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACgccgcc                                                                                                                         >  2:1074300/1‑139 (MQ=255)

             gAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCa                                                                                                            >  2:837909/1‑139 (MQ=255)

             gAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCa                                                                                                            >  2:1441267/1‑139 (MQ=255)

              aaCACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCaa                                                                                                           >  2:1004147/1‑139 (MQ=255)

                  ccAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTg                                                                                                       <  1:1074300/139‑1 (MQ=255)

                          atCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTc                                                                                               >  1:1159922/1‑139 (MQ=255)

                                gCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTg                                                                                         >  2:1438587/1‑139 (MQ=255)

                                gCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTg                                                                                         >  1:1200031/1‑139 (MQ=255)

                                gCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTg                                                                                         >  1:1193908/1‑139 (MQ=255)

                                     cGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGc                                                                                    >  2:46842/1‑139 (MQ=255)

                                     cGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGc                                                                                    >  2:1422227/1‑139 (MQ=255)

                                        cAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGAt                                                                                 <  1:711568/139‑1 (MQ=255)

                                                    tAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCa                                                                     <  1:1004147/139‑1 (MQ=255)

                                                    tAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCa                                                                     <  2:1193908/139‑1 (MQ=255)

                                                    tAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCa                                                                     <  2:1200031/139‑1 (MQ=255)

                                                                  gcgcATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGt                                                       <  1:1438587/139‑1 (MQ=255)

                                                                           aCGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGt                                              <  1:1422227/139‑1 (MQ=255)

                                                                           aCGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGt                                              <  1:837909/139‑1 (MQ=255)

                                                                               ctctTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             <  1:1273957/136‑1 (MQ=255)

                                                                               ctctTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             >  2:1273957/1‑136 (MQ=255)

                                                                                  tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                          >  2:139551/1‑57 (MQ=255)

                                                                                  tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                          <  1:139551/57‑1 (MQ=255)

                                                                                  tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                            >  2:227597/1‑86 (MQ=255)

                                                                                  tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                            <  1:227597/86‑1 (MQ=255)

                                                                                  tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTAc                                       >  2:229728/1‑139 (MQ=255)

                                                                                     gCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGa                                    <  1:1441267/139‑1 (MQ=255)

                                                                                         tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             >  2:700297/1‑126 (MQ=255)

                                                                                         tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             <  1:700297/126‑1 (MQ=255)

                                                                                         tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGatcat                                >  1:875281/1‑139 (MQ=255)

                                                                                          gCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGAt                                                                                 >  1:98436/1‑89 (MQ=255)

                                                                                          gCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGAt                                                                                 <  2:98436/89‑1 (MQ=255)

                                                                                          gCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             <  1:767823/125‑1 (MQ=255)

                                                                                          gCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                             >  2:767823/1‑125 (MQ=255)

                                                                                                     ggCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGatcat                                >  2:1420479/1‑127 (MQ=255)

                                                                                                     ggCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGatcat                                <  1:1420479/127‑1 (MQ=255)

                                                                                                     ggCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGaaa                    <  2:875281/139‑1 (MQ=255)

                                                                                                          cGACTGCAACAACGCCGCCGCCGTTAACGCCGcccc                                                                                                                       >  1:513185/1‑36 (MQ=255)

                                                                                                          cGACTGCAACAACGCCGCCGCCGTTAACGCCGcccc                                                                                                                       <  2:513185/36‑1 (MQ=255)

                                                                                                           gACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGAt                                                                       >  2:1280789/1‑82 (MQ=255)

                                                                                                           gACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGAt                                                                       <  1:1280789/82‑1 (MQ=255)

                                                                                                           gACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGt              <  1:654862/139‑1 (MQ=255)

                                                                                                             cTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTa            <  2:1159922/139‑1 (MQ=255)

                                                                                                                       gccgccgccGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGc  <  1:229728/139‑1 (MQ=255)

                                                                                                                           ccgccgTTAACGCCG‑CCCCTGTAACAGCAAGGTgcgc                                                                                                    <  1:844081/37‑1 (MQ=37)

                                                                                                                           ccgccgTTAACGCCG‑CCCCTGTAACAGCAAGGTgcgc                                                                                                    >  2:844081/1‑37 (MQ=37)

CGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCGCCCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGC  >  NC_000913/3849650‑3849908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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