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 F174 I0 R1	55	81.0	1740380	95.7%	1665543	141.0

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%	127.3 / ‑6.5	44	S204L (TCA→TTA)	USA300HOU_1186	CodY family transcriptional regulator
Reads supporting (aligned to +/- strand): ref base C (1/1); major base T (14/26); minor base G (0/2); total (15/29)
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.

GAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAA  >  CP000730/1274078‑1274339

gAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAAGCGCATTAAAAGTTGCa                                                                                                                           <  1:480949/141‑1 (MQ=255)

aaaGTAGAGAAAGGAGCGCGCGATAAAGCTGCTAGTACAATGACAATTAATGTATTATTATATCCTGAAAACGAACCGATTTAACATATCTTTGGAAAACTTGGCGTGACGGAAGGCCTATTAATCGCATTAAAAGTTGCa                                                                                                                           <  2:419802/140‑1 (MQ=255)

  aGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGa                                                                                                                         <  2:326837/141‑1 (MQ=255)

  aGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGa                                                                                                                         <  1:709542/141‑1 (MQ=255)

     aGAAAAAGAAGCGCGCGATAAGGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGACGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATag                                                                                                                      <  2:466763/141‑1 (MQ=255)

       aaaaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTagag                                                                                                                    >  2:533233/1‑141 (MQ=255)

        aaaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGt                                                                                                                   >  1:761085/1‑141 (MQ=255)

          aagaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTATGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGAAGCTAGGGTTg                                                                                                                 >  2:512776/1‑141 (MQ=255)

             aagCGCGTGATAAAGCTGCTATTACAATGGCAATTAATTCATTATTTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGTCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTa                                                                                                              <  2:404724/141‑1 (MQ=255)

               gcgcgcGATAAAGCTGCTATTACAATGGCAATTAATTCATCATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACAGAAGGCCGATTAATCGCATTAAAAGTTGCCGATAGAGTTgggctt                                                                                                            >  2:818486/1‑137 (MQ=255)

                cgcgtgATAAAGCTGCTATTACGAGGGCAATTAATGTAGTAGTGGATCTTAGAACAATTGCGATTGTACGTACCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATGAAAAGTTGCATATAGATTTGGTATTa                                                                                                           <  2:93201/141‑1 (MQ=255)

                cgcgcgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCAGTACGTAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTa                                                                                                           >  2:830028/1‑141 (MQ=255)

                    cgATTAAGCTGCTATTACAATGCCAATTATTTCATTATCATATTGTGTCGAGGTAGCTTGGGAACATAGCGGTGAAGAGCTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGGTGCGGATAGAGTTGGTATTACGAg                                                                                                       <  2:48741/141‑1 (MQ=255)

                        aaaGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCGGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCt                                                                                                   <  1:447040/141‑1 (MQ=255)

                         aaGCTGCTATTACAAGGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAACACTTTCTGATGGAGGGGGTATTACTAGATCTg                                                                                                  <  1:206955/141‑1 (MQ=255)

                            ctgctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                               <  1:836994/141‑1 (MQ=255)

                              tctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGTTCTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAAtt                                                                                             <  2:742231/140‑1 (MQ=255)

                              gctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAAtt                                                                                             <  1:742821/141‑1 (MQ=255)

                                  ttACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGCACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTaa                                                                                         <  1:584839/141‑1 (MQ=255)

                                     aaaTGGCAATTAATTCATTATCTTATGCTGAAAAAGAAGCGATTGAACATATCGTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATg                                                                                      <  2:753094/140‑1 (MQ=255)

                                        tGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                   <  1:469580/141‑1 (MQ=255)

                                           cAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTAc                                                                                >  1:770821/1‑141 (MQ=255)

                                             attaattCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGt                                                                              <  2:321470/141‑1 (MQ=255)

                                                  ttCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAAtt                                                                         <  2:323167/141‑1 (MQ=255)

                                                    taatATCTCATTCTAAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGACTATTAATCGTATTAAAAGTTTAAGATAGAGTTAGTATTAGTAGATCTGTAATTTTAAATGCACTACGTAAATTAg                                                                       <  2:454166/138‑1 (MQ=255)

                                                    cATTATCTTGTTCAGAAAAAGAAGCGATTGAACATATCGTTGAAGAACTTGGTGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGTTATTACTAGATCTGTAATTGTAGATGCACTACGTAGATTAg                                                                       <  2:495868/141‑1 (MQ=255)

                                                    cATGATCTTATTCTGAAAAAGAAGCGATTGAACGTATCTTTGAAGAACGTGGGGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAg                                                                       <  2:42859/141‑1 (MQ=255)

                                                     aTTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGa                                                                      >  1:150822/1‑141 (MQ=255)

                                                               tCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTTCTGgt                                                            <  2:529421/141‑1 (MQ=255)

                                                                        gaagCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGAAAGAGTTGGTATTACTCGATCTGTAATTGGACATGCACTACGTAAATTAGAAAGTGCTGGTGAAATTGaa                                                   >  2:29845/1‑141 (MQ=255)

                                                                             gATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACg                                              >  2:318538/1‑141 (MQ=255)

                                                                                 gAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAGTTGAATCACGTTCt                                          >  1:774834/1‑141 (MQ=255)

                                                                                          tttGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATg                                 >  1:509457/1‑141 (MQ=255)

                                                                                                   cTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGGATGGAAGGTACt                        >  2:454555/1‑141 (MQ=255)

                                                                                                   cTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                        <  2:747325/141‑1 (MQ=255)

                                                                                                   cTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                        <  2:69302/141‑1 (MQ=255)

                                                                                                   cTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                        <  2:226723/141‑1 (MQ=255)

                                                                                                           tACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaa                <  1:353072/141‑1 (MQ=255)

                                                                                                            tgggAAGGCCTATTAAACGCTTTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaaa               <  2:401904/139‑1 (MQ=255)

                                                                                                             cGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTATTTAGGAATGAAAGGGACTTTCATTAAAg              >  1:369840/1‑141 (MQ=255)

                                                                                                              ggAAGGCCTATTAATAGCATTAAAGGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGGAAGGTACTTTCATTAAAGt             <  2:409519/141‑1 (MQ=255)

                                                                                                                 aGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAGTTGGGTCTCGTGCTTTAGGAATGAAAGGTACTTTCCTTAAGGTGaa          >  1:668769/1‑141 (MQ=255)

                                                                                                                  ggCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTaaa         >  1:20243/1‑141 (MQ=255)

                                                                                                                         tAATCGCACGAAAAGTGCGAGATGTAGTTGTTATTACTAGATCTTGAATTGTAAATGCACTACGTAAATTAGAAAGTGCTTGTGTAATTGAATCACGTTTTTTAGGAATTAAAGGTACTTTCATTAAAGTTAAAAAAGaaa  <  2:735745/141‑1 (MQ=255)

GAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAA  >  CP000730/1274078‑1274339

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A