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 F110 I0 R1	50	71.1	1529928	95.4%	1459551	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,274,208	C→T	100%	S204L (TCA→TTA)	USA300HOU_1186 →	CodY family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,274,208	0	C	T	100.0%	154.6 / ‑6.5	49	S204L (TCA→TTA)	USA300HOU_1186	CodY family transcriptional regulator
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (22/26); minor base A (1/0); total (23/26)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTC  >  CP000730/1274077‑1274344

tGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGc                                                                                                                                 <  2:426968/141‑1 (MQ=255)

        aaaaaGAAGCGCGCGATAAAGCTGCTATTAGAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTGGAAGAACTTGGCGGTACGGGAGGCCTATTAATCGCATTAAAAGTTGCAGATagag                                                                                                                         <  2:333752/141‑1 (MQ=255)

         aaaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGt                                                                                                                        <  1:658274/141‑1 (MQ=255)

         aaaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGt                                                                                                                        <  1:736475/141‑1 (MQ=255)

          aaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGtt                                                                                                                       <  2:467464/141‑1 (MQ=255)

           aagaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTg                                                                                                                      <  1:362431/141‑1 (MQ=255)

                 cgcgcgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTa                                                                                                                >  2:313184/1‑141 (MQ=255)

                   cgcgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACt                                                                                                              >  1:131382/1‑141 (MQ=255)

                       aTAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGAt                                                                                                          <  1:757036/141‑1 (MQ=255)

                       aTAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTATGAAAAAGAAGCGATTGAACATATCTTTGACGAACTTGGCGGTACGGAAGGCCTGTTAATGGCGTTAAAAGTTGCAGATAGAGTTGGTATTACTAggt                                                                                                          >  1:214903/1‑139 (MQ=255)

                        tAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATc                                                                                                         <  2:94443/141‑1 (MQ=255)

                        aaaaGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATc                                                                                                         <  2:392687/140‑1 (MQ=255)

                          aaGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATAACAAGTTGCAGATAGAGTTGGTATTACTAGATCTg                                                                                                       >  1:722050/1‑141 (MQ=255)

                           aGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGTTAGAGTTGGTATTACTAGATCTGt                                                                                                      >  1:227958/1‑141 (MQ=255)

                                ctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTg                                                                                                 <  2:541488/141‑1 (MQ=255)

                                    tACAATGGCAAATAATTCATTAGCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTaaa                                                                                             <  1:69990/141‑1 (MQ=255)

                                    tACAACGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAAGCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTaaa                                                                                             <  2:204224/141‑1 (MQ=255)

                                      cAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATg                                                                                           >  1:331393/1‑141 (MQ=255)

                                       aaTGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGc                                                                                          >  1:324473/1‑141 (MQ=255)

                                        aTGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCa                                                                                         >  2:418887/1‑141 (MQ=255)

                                         tGGCAATTAATTCATTATCTTGTTCTGAAAAAGAAGCGATTGAACATTTCTTTCAAGAACTTGGCAGTACGGAAGGCCTATTAATCGCATTAAAGTTTGCAGTTAGAGTTGGTAATACTAGATCTGTAAGTGTAAATTCAc                                                                                        <  2:135607/141‑1 (MQ=255)

                                           gCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGACCCCGGAAGGTTTGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTa                                                                                      <  1:360717/141‑1 (MQ=255)

                                            cAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTAc                                                                                     <  2:65439/141‑1 (MQ=255)

                                              attaattCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGt                                                                                   >  2:511443/1‑141 (MQ=255)

                                                taattCATTATCTTATTCGGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATGAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTaa                                                                                 <  2:364242/141‑1 (MQ=255)

                                                      aTTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGa                                                                           >  1:236834/1‑141 (MQ=255)

                                                               ttCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTgg                                                                  >  1:425791/1‑141 (MQ=255)

                                                                    aaaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCCCTACGTAAATTAGAAAGTGCTGGTGTaa                                                             >  1:521300/1‑141 (MQ=255)

                                                                           agCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATc                                                      >  1:236698/1‑141 (MQ=255)

                                                                           agCGAGTGAACAGATCTTTGAAGCACTTGGCGGTACGGAAGGCCTATTAAGCGCACTAAAAGTTGCAGATAGAGGTGGTATTACTAGATCTGTAATTATAACTGCACTACGTAAATGAGAAAGTGCTGCTGTGCTTGCATc                                                      >  2:475169/1‑141 (MQ=255)

                                                                               aTTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGt                                                  <  1:313184/141‑1 (MQ=255)

                                                                                 tGAACATATCTATGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATAACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTc                                                <  1:303501/141‑1 (MQ=255)

                                                                                    aCATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAACTTGCAGATAGGGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCttt                                             <  2:47465/141‑1 (MQ=255)

                                                                                       tatCTTTGAAGAACATGGCAGTACGGAAGGCCTATTCATCGCATTAAAAGTTGCAGATACAGTTGGTATTACTAGATCTGTAGTTGTAAATGCACTACGTGAATTAGTAAGTGCTGGTGTACTTGAATTACGTTCTTTAgg                                          >  2:424625/1‑141 (MQ=255)

                                                                                        atCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGa                                         <  2:331393/141‑1 (MQ=255)

                                                                                          cTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAAt                                       <  1:590924/141‑1 (MQ=255)

                                                                                            ttGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGGTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTTGGAATGa                                     >  2:671823/1‑141 (MQ=255)

                                                                                                 gaaCTTGGCGGTAGGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATGGAGGTGGTATTACTAGATGTGTAATTGTAAATGCACTACGTAGATTAGAAAGTGCTGGTGTAATTGAATCAGGTTCTTGAGGAGTGAGAGGt                                >  1:189498/1‑141 (MQ=255)

                                                                                                 gaaCTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGGGCTGGTGTAATTGAATCACGTTTTTTAGGAATGAAAGGt                                >  2:668961/1‑141 (MQ=255)

                                                                                                   aCTTGGCGGCACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTAc                              >  2:408053/1‑141 (MQ=255)

                                                                                                    cTTGGCGGTACGGAAGTCATATTAAGCGCATTAAAAGTGTCAGATCGGGTTGTGATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAgtacct                             <  1:746012/141‑6 (MQ=255)

                                                                                                          ggTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAATGGTACtttaaaa                       <  2:394314/141‑5 (MQ=255)

                                                                                                          ggTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCAtt                       <  2:432144/141‑1 (MQ=255)

                                                                                                                  aGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTaa               >  1:291635/1‑141 (MQ=255)

                                                                                                                      cTATTAATCGCATTAAAAGTCGCAGATAGAGTTGTTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGTTGTAATTGAATCACGTTCTTTAGTAATGAAAGGTACTTTCATTAAAGTTaaaaaa           <  2:577624/141‑1 (MQ=255)

                                                                                                                          tAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACCACGTAAATTAGCAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGaaa       <  2:381240/141‑1 (MQ=255)

                                                                                                                             tCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAAt    >  1:358549/1‑141 (MQ=255)

                                                                                                                              cGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGaaaaaat   >  2:710253/1‑139 (MQ=255)

                                                                                                                               gCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAAttt  >  1:478269/1‑140 (MQ=255)

TGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTC  >  CP000730/1274077‑1274344

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A