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 I2 R1	766	55.6	2631458	94.7%	2491990	109.9

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%	151.0 / NA	37	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 . (16/21); total (16/21)

CGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCGCCCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCG  >  NC_000913/3849650‑3849913

cGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                               <  2:79521/139‑1 (MQ=255)

cGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                               >  2:326153/1‑139 (MQ=255)

  agaTAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCGccc                                                                                                                             >  2:971316/1‑139 (MQ=255)

         gCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAAc                                                                                                                     >  1:449912/1‑139 (MQ=255)

                cacCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAgg                                                                                                              <  1:326153/139‑1 (MQ=255)

                  ccAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAACAAGGTg                                                                                                            >  1:439596/1‑139 (MQ=255)

                   cAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                               >  1:1071737/1‑120 (MQ=255)

                   cAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAAcgccgc                                                                                                                               <  2:1071737/120‑1 (MQ=255)

                   cAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTgc                                                                                                           >  1:21472/1‑139 (MQ=255)

                           tCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCa                                                                                                   >  2:121054/1‑139 (MQ=255)

                             ggggCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                                 <  1:971316/139‑1 (MQ=255)

                               ggCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCt                                                                                               <  2:449912/139‑1 (MQ=255)

                               ggCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCt                                                                                               >  1:526775/1‑139 (MQ=255)

                                 ccAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGa                                                                                             >  2:371081/1‑139 (MQ=255)

                                         aGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACgccgcc                                                                                                                              >  2:979804/1‑99 (MQ=255)

                                         aGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACgccgcc                                                                                                                              <  1:979804/99‑1 (MQ=255)

                                                         tCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCt                                                                     <  2:501250/139‑1 (MQ=255)

                                                             cAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCCGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                                 >  2:300950/1‑107 (MQ=255)

                                                             cAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                                 <  1:300950/107‑1 (MQ=255)

                                                             cAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACgg                                                                 >  1:212092/1‑139 (MQ=255)

                                                                cAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCa                                                              <  1:480080/139‑1 (MQ=255)

                                                                cAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCa                                                              <  2:21472/139‑1 (MQ=255)

                                                                  gcgcATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGt                                                            >  1:654649/1‑139 (MQ=255)

                                                                     cATTCCACGACGCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTACCAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAAc                                                         <  1:560510/139‑1 (MQ=255)

                                                                            cGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                                  <  2:948835/139‑1 (MQ=255)

                                                                            cGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                                  <  2:671010/139‑1 (MQ=255)

                                                                            cGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAACAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                                  <  2:439596/139‑1 (MQ=255)

                                                                               ctctTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                                 >  1:970727/1‑89 (MQ=255)

                                                                               ctctTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACg                                                                                                 <  2:970727/89‑1 (MQ=255)

                                                                                 ctTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTa                                             >  2:255704/1‑139 (MQ=255)

                                                                                  tttGCCGTGCCAAAGTCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTAc                                            >  1:912627/1‑139 (MQ=255)

                                                                                  tttGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTGACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTAc                                            >  1:694738/1‑139 (MQ=255)

                                                                                         tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCt                                                                                               >  2:78306/1‑81 (MQ=255)

                                                                                         tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCt                                                                                               <  1:78306/81‑1 (MQ=255)

                                                                                         tGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGatcat                                     <  2:694738/139‑1 (MQ=255)

                                                                                          gCCAAAGTCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGatcatc                                    <  2:912627/139‑1 (MQ=255)

                                                                                                     ggCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGaaa                         <  1:156126/139‑1 (MQ=255)

                                                                                                     ggCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGaaa                         <  1:567651/139‑1 (MQ=255)

                                                                                                               gCAACAACGCCGCCGCCGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTaaa               <  2:526775/139‑1 (MQ=255)

                                                                                                                       gccgccgccGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                                  >  2:1170440/1‑96 (MQ=255)

                                                                                                                       gccgccgccGTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTa                                                  <  1:1170440/96‑1 (MQ=255)

                                                                                                                            cgccgTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCg  <  2:886624/139‑1 (MQ=255)

                                                                                                                              ccgTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCa                                                                          >  2:1312678/1‑65 (MQ=255)

                                                                                                                              ccgTTAACGCCG‑CCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCa                                                                          <  1:1312678/65‑1 (MQ=255)

CGAGATAGTGCCAGAACACCAGACATATCGGGGCCAGCGTCAGGCCGCCAGTTAAAGTCAGCAACAGCGCATTCCACGACTCTTTGCCGTGCCAAAGCCAGGGCAGCGACTGCAACAACGCCGCCGCCGTTAACGCCGCCCCCTGTAACAGCAAGGTGCGCCAGTCACGCTGATGGCGATAGCGCGAGATCAGCGCTACGGGCAGTAACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCG  >  NC_000913/3849650‑3849913

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A