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
A15 F177 I1 R2	35	38.3	831348	95.5%	793937	139.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,679,650	G→A	C45Y (TGT→TAT)	cbpD →	possible secretory antigen

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,679,650	0	G	A	100.0%	92.1 / NA	29	C45Y (TGT→TAT)	cbpD	possible secretory antigen
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (14/15); total (14/15)

AAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATT  >  CP000730/2679515‑2679779

aaaTGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACAt                                                                                                                              <  1:311962/141‑1 (MQ=255)

   tGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCAGCAGTTAATTATTATAGTAAAAACCAATATACAtggt                                                                                                                           >  2:184854/1‑141 (MQ=255)

      aaTATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTggg                                                                                                                        <  2:282585/141‑1 (MQ=255)

         ataAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCAt                                                                                                                     >  2:89329/1‑141 (MQ=255)

                              tattaATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCAC‑TATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCgg                                                                                               <  2:16224/141‑1 (MQ=255)

                                ttaATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATGAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGt                                                                                              >  2:181676/1‑141 (MQ=255)

                                     tGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAAACCGTCGACCAAACGCTGCCCTGATATTGCGGGGTTTAGTAGTATATTTGAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAAcc                                                                                         >  1:80488/1‑141 (MQ=255)

                                       cTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTg                                                                                       >  2:367634/1‑141 (MQ=255)

                                           tGCAGTACTTTTCACAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATAATAGAAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTc                                                                                   <  2:345750/141‑1 (MQ=255)

                                            gCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACAtggtgg                                                                                                                         >  2:237741/1‑102 (MQ=255)

                                            gCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACAtggtgg                                                                                                                         <  1:237741/102‑1 (MQ=255)

                                              aGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTaa                                                                                <  1:368021/141‑1 (MQ=255)

                                                       ctcAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATgggg                                                                       >  2:148649/1‑141 (MQ=255)

                                                         cagcagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCa                                                                     >  1:64620/1‑141 (MQ=255)

                                                            cagATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATg                                                                  <  1:232876/141‑1 (MQ=255)

                                                                  tCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTaaaa                                                            >  1:157754/1‑141 (MQ=255)

                                                                               cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAATCCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACaa                                               <  1:271820/141‑1 (MQ=255)

                                                                                 tCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATg                                             >  2:223096/1‑141 (MQ=255)

                                                                                  cGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGc                                            <  2:233861/141‑1 (MQ=255)

                                                                                     aCAAACGCATCAATCGCATGCCGAGTTTAATTATTAGAGTAAAAAACTATATAGATAGAAGGAAAATAAAAGTTGCGGACAAGGCGGTAAACATGTTTCTAGTAGATGGTACAATGCTAAAAATTGGTATTaggatgaaaa                                         <  2:212942/141‑10 (MQ=255)

                                                                                           gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATc                                   <  2:177281/141‑1 (MQ=255)

                                                                                            cATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCa                                  <  2:157754/141‑1 (MQ=255)

                                                                                                aaTCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAat                              >  2:280407/1‑141 (MQ=255)

                                                                                                aaTCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAat                              >  2:42137/1‑141 (MQ=255)

                                                                                                    gCATGCCGCAGTTAATTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGc                          >  2:92888/1‑141 (MQ=255)

                                                                                                      aTGCCGCAGTCAAGTATTATAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAACATATGCGa                        >  2:83904/1‑141 (MQ=255)

                                                                                                                    tattatAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCa          <  1:174258/141‑1 (MQ=255)

                                                                                                                    tattatAGTAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCa          <  1:174257/141‑1 (MQ=255)

                                                                                                                            tAAAAACCAATATACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAAtt  <  1:162355/141‑1 (MQ=255)

AAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATT  >  CP000730/2679515‑2679779

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A