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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,974,824	C→T	L167L (CTG→CTA)	cheA ←	fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,974,824	0	C	T	100.0%	107.7 / NA	34	L167L (CTG→CTA)	cheA	fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (20/14); total (20/14)

AGTACCGCTGTGATGTCATCTTCGGCGATGTCGCCCGGTAATATTGCCGAGAGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTCAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCGGGTCACTGCGGATGGCGTTTCGCCTTTCGCTTCTAAT  >  NC_000913/1974690‑1974944

agTACCGCTGTGATGTCATCTTCGGCGATGTCGCCCGGTAATATTGCCGAGAGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGgc                                                                                                                      >  2:1074922/1‑139 (MQ=255)

    ccGCTGTGATGTCATCTTCGGCGATGTCGCCCGGTAATATTGCCGAGAGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGa                                                                                                                  <  1:85589/139‑1 (MQ=255)

          tgATGTCATCTTCGGCGATGTCGCCCGGTAATATTGCCGAGAGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGAt                                                                                                            >  2:983995/1‑139 (MQ=255)

                                 cccGGTAATATTGCCGAGAGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGc                                                                                     >  1:377441/1‑139 (MQ=255)

                                        atatTGCCGAGAGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTg                                                                              >  2:450285/1‑139 (MQ=255)

                                            tGCCGAGAGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCa                                                                          >  1:1015467/1‑139 (MQ=255)

                                                gagaGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCtt                                                                      >  2:499811/1‑139 (MQ=255)

                                                      gAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGtt                                                                <  1:499811/139‑1 (MQ=255)

                                                       aaTCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCgcgg                                                                                                >  2:723410/1‑106 (MQ=255)

                                                       aaTCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCgcgg                                                                                                <  1:723410/106‑1 (MQ=255)

                                                             ccccTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACtttt                                                         <  1:963064/139‑1 (MQ=255)

                                                                  ttCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCaa                                                    >  1:393449/1‑139 (MQ=255)

                                                                          gTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACtt                                            >  1:671478/1‑139 (MQ=255)

                                                                            cAGTTAACGTTGTCAGATGTCCCAGTTCTGCTTCCAGCAGGTCGAGTTCCCCGGCCTTTAGGCGCGCAAGGATAATTCGTCGCGTCGCCTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTaa                                          >  2:654677/1‑139 (MQ=255)

                                                                                       gTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCggg                                     <  2:767262/133‑1 (MQ=255)

                                                                                       gTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACGTTTGGCAACCACACTTAATCggg                                     >  1:767262/1‑133 (MQ=255)

                                                                                         cAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACcaca                                               >  1:355301/1‑121 (MQ=255)

                                                                                         cAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACcaca                                               <  2:355301/121‑1 (MQ=255)

                                                                                             tGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCGGGTCACTGCGGATg                         <  1:450285/139‑1 (MQ=255)

                                                                                              gTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCGGGTCACTGCGGATgg                        >  2:733746/1‑139 (MQ=255)

                                                                                                cccAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCga                                                                                             >  1:144620/1‑68 (MQ=255)

                                                                                                cccAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCga                                                                                             <  2:144620/68‑1 (MQ=255)

                                                                                                          cttcCAGCAGGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCGGGTCACTGCGGATGGCGTTTCGCCttt            >  1:313754/1‑139 (MQ=255)

                                                                                                               agcagGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGt                                                                 >  2:17253/1‑81 (MQ=255)

                                                                                                               agcagGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGt                                                                 <  1:17253/81‑1 (MQ=255)

                                                                                                               agcagGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCGGGTCACTGCGGATGGCGTTTCGCCTTTCGCtt       <  2:313754/139‑1 (MQ=255)

                                                                                                                gcagGTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCGGGTCACTGCGGATGGCGTTTCGCCTTTCGCTTc      <  2:1015467/139‑1 (MQ=255)

                                                                                                                    gTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATtcgtcg                                                                                                   >  1:801322/1‑42 (MQ=255)

                                                                                                                    gTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATtcgtcg                                                                                                   <  2:801322/42‑1 (MQ=255)

                                                                                                                    gTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGa                                                                                   >  1:770920/1‑58 (MQ=255)

                                                                                                                    gTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGa                                                                                   <  2:770920/58‑1 (MQ=255)

                                                                                                                    gTCGACTTCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCGGGTCACTGCGGATGGCGTTTCGCCTTTCGCTTCTAAt  >  1:1028968/1‑139 (MQ=255)

                                                                                                                           tCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGa                                                                                   <  2:109358/51‑1 (MQ=255)

                                                                                                                           tCCCCGGCCTTTAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGa                                                                                   >  1:109358/1‑51 (MQ=255)

AGTACCGCTGTGATGTCATCTTCGGCGATGTCGCCCGGTAATATTGCCGAGAGCGAATCCGCCCCTTTCACCACGTCAGTTAACGTTGTCAGATGTCCCAGTTCTTCTTCCAGCAGGTCGACTTCCCCGGCCTTCAGGCGCGAAAGGATAATTCGTCGCGGCGACTGACTGCGACTCTGCTCATCTTGCGGTTCACTTTTGGCAACCACACTTAATCGGGTCACTGCGGATGGCGTTTCGCCTTTCGCTTCTAAT  >  NC_000913/1974690‑1974944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A