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
A9 F1 I2 R1	760	52.7	2744488	90.2%	2475528	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	586,280	T→C	N210S (AAC→AGC)	envY ←	porin thermoregulatory transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	586,280	0	T	C	100.0%	134.4 / NA	38	N210S (AAC→AGC)	envY	porin thermoregulatory transcriptional activator
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/21); total (17/21)

TCACTTTTTGTCGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGTTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTGGGGCTTAAACATAGCGAACT  >  NC_000913/586155‑586401

tCACTTTTTGTCGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATaa                                                                                                              >  1:650152/1‑139 (MQ=255)

   cTTTTTGTCGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACAt                                                                                                           >  1:2192/1‑139 (MQ=255)

      tttGTCGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAACCGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTg                                                                                                        >  2:778078/1‑139 (MQ=255)

               gTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTa                                                                                               <  2:693969/139‑1 (MQ=255)

               gTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTa                                                                                               <  1:393450/139‑1 (MQ=255)

               gTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTa                                                                                               <  1:235772/139‑1 (MQ=255)

                  tGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACg                                                                                            <  2:550375/139‑1 (MQ=255)

                      gagaTAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATa                                                                                        <  2:968340/139‑1 (MQ=255)

                         aTAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGTTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGa                                                                                     <  1:1306033/139‑1 (MQ=255)

                         aTAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGa                                                                                     <  1:439256/139‑1 (MQ=255)

                         aTAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGa                                                                                     <  2:650152/139‑1 (MQ=255)

                             ttCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACAct                                                                                 <  2:760033/139‑1 (MQ=255)

                                     tgtCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATcc                                                                                                                      <  1:1327006/94‑1 (MQ=255)

                                     tgtCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATcc                                                                                                                      >  2:1327006/1‑94 (MQ=255)

                                       tCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAAt                                                                                                                <  2:886355/98‑1 (MQ=255)

                                       tCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAAt                                                                                                                >  1:886355/1‑98 (MQ=255)

                                        cAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATc                                                                      >  2:700209/1‑139 (MQ=255)

                                               tAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATaa                                                                                                              <  1:1181828/92‑1 (MQ=255)

                                               tAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATaa                                                                                                              >  2:1181828/1‑92 (MQ=255)

                                               tAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCtat                                                               >  2:631550/1‑139 (MQ=255)

                                                  accGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGc                                                            <  1:778078/137‑1 (MQ=255)

                                                                              acgTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCttttt                                >  2:337091/1‑139 (MQ=255)

                                                                                 tgctgcTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGaca                                                                                   >  1:434537/1‑85 (MQ=255)

                                                                                 tgctgcTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGaca                                                                                   <  2:434537/85‑1 (MQ=255)

                                                                                 tgctgcTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAg                             <  1:337091/139‑1 (MQ=255)

                                                                                 tgctgcTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAg                             <  1:700209/139‑1 (MQ=255)

                                                                                 tgctgcTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAg                             >  1:6757/1‑139 (MQ=255)

                                                                                       tataGCCACATAATTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCt                       <  1:631550/139‑1 (MQ=255)

                                                                                                aTAATTGCGCCACCTGAGTGATATTTTTGCTATccc                                                                                                                     >  2:498278/1‑35 (MQ=255)

                                                                                                aTAATTGCGCCACCTGAGTGATATTTTTGCTATCCa                                                                                                                     <  1:498278/36‑1 (MQ=255)

                                                                                                   aTTGCGCCACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTGGGGCTTAAACa           >  1:265775/1‑139 (MQ=255)

                                                                                                         ccACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTg                      >  1:1180017/1‑122 (MQ=255)

                                                                                                         ccACCTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTg                      <  2:1180017/122‑1 (MQ=255)

                                                                                                            ccTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCAt                                                                                         <  1:1029056/52‑1 (MQ=255)

                                                                                                            ccTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCAt                                                                                         >  2:1029056/1‑52 (MQ=255)

                                                                                                            ccTGAGTGATATTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTGGGGCTTAAACATAGCGAACt  >  1:1356753/1‑139 (MQ=255)

                                                                                                                    atatTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCt                                                                 <  1:722249/68‑1 (MQ=255)

                                                                                                                    atatTTTTGCTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCt                                                                 >  2:722249/1‑68 (MQ=255)

TCACTTTTTGTCGCTGTTTGGCGAGATAATTCAACGGTGTCAGGCCGTAAAACGCCTTAAAAACAGAGATAAAGTACGACGTGCTGCTATAGCCACATAATTGCGCCACCTGAGTGATATTTTTGTTATCCATCAATAACATCTGTACGGCGTAACGCATACGACACTCTGTGACAATCTGGCTATAGCTGGTATTTTCGTTTTTTAATTTCTTTTTGAGCAGGCTGGGGCTTAAACATAGCGAACT  >  NC_000913/586155‑586401

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