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 F104 I0 R1	54	57.6	1336546	96.4%	1288430	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,362	G→A	100%	H104Y (CAC→TAC)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,362	0	G	A	100.0%	104.5 / NA	35	H104Y (CAC→TAC)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (15/20); total (15/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCC  >  USA300TCH1516_ALE/1744230‑1744485

ttATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTa                                                                                                                     >  2:511083/1‑141 (MQ=255)

    acaTGCAATACCTTCTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAAc                                                                                                                 <  2:284746/139‑1 (MQ=255)

     aaTGCAATCCCTACTACTATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACa                                                                                                                <  2:147608/141‑1 (MQ=255)

     aaTGCAATACATACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACa                                                                                                                <  2:269143/141‑1 (MQ=255)

       tGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACAtt                                                                                                              >  1:133887/1‑141 (MQ=255)

             aCCTACTACGTTACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTAcc                                                                                                        <  1:22278/141‑1 (MQ=255)

              ccTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCa                                                                                                       <  1:295647/141‑1 (MQ=255)

                          ccGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                           <  1:620948/141‑1 (MQ=255)

                               tAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCCTCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTc                                                                                      <  2:500474/141‑1 (MQ=255)

                               tAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTc                                                                                      <  1:86844/141‑1 (MQ=255)

                                   ttttCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTAATTTACATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATaa                                                                                  <  1:624711/141‑1 (MQ=255)

                                     ttCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTACTCGATCTTGTTTAATTAACACACGTTGACCTGTTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACg                                                                                <  1:481378/141‑1 (MQ=255)

                                        aaCTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAAt                                                                             >  1:398927/1‑141 (MQ=255)

                                             aTTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACtt                                                                        >  1:535086/1‑141 (MQ=255)

                                                 tATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTTTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACg                                                                    >  1:76272/1‑141 (MQ=255)

                                                  aTTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGa                                                                   <  1:183345/141‑1 (MQ=255)

                                                  aTTGCCGCTTCAATCGTACCACCAGTAGCTAATAAATCATTTGTAATTAACTCACGTTGGCCTGGTTTAATTGCATCTTTTGACATTGTTAAAACATTTGTACCTTTTTCTAGGTCATACTCATAACGAATGACTTCAcaa                                                                   <  2:207951/141‑3 (MQ=255)

                                                   ttGCTGCTCCAATCATACCACCAGTAGCTAATAAATCTTCTGTAATTAACACACGTTGACCTGGTTTACTTGCATCTTTTTACCATTTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAg                                                                  <  2:605298/141‑1 (MQ=255)

                                                     gctgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGt                                                                >  1:512266/1‑141 (MQ=255)

                                                               tCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCctt                                                      >  1:293686/1‑141 (MQ=255)

                                                                cGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCcttc                                                     >  1:10448/1‑141 (MQ=255)

                                                                         aGTAGCTAATAAATCATCTGTAATTAACACACGTGGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                            <  1:217767/141‑1 (MQ=255)

                                                                           tAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGGTTAATTGCATCTTTGTACATTGTTAAAACATGTGTACCATATCCTGGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAg                                          <  2:3381/141‑1 (MQ=255)

                                                                            aGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAgg                                         <  2:560839/141‑1 (MQ=255)

                                                                              cTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAAGTg                                       >  1:476349/1‑141 (MQ=255)

                                                                              cTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGAACCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTg                                       >  2:240037/1‑141 (MQ=255)

                                                                                   aaaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAg                                  >  2:508191/1‑141 (MQ=255)

                                                                                   aaaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTAATAACGCATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAg                                  >  2:69969/1‑141 (MQ=255)

                                                                                        atcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAAt                             >  1:582135/1‑141 (MQ=255)

                                                                                            gTAATTAACCCACGTTGACCTGGTTTAATTGCATCTCTGTACATTGTCGCTGCTTTGGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATcccc                         <  1:19084/141‑1 (MQ=255)

                                                                                            gTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATcccc                         <  1:299839/141‑1 (MQ=255)

                                                                                                   acacacGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAAt                  <  2:512266/141‑1 (MQ=255)

                                                                                                     acacGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATACTCTAGGTCATACTCATAACGAATGACTTCACGCGGTAATTTCCCTTCTTATCAAACTGGAGCAAAGCCAAGCCCCAGTGAATaa                >  2:153593/1‑141 (MQ=255)

                                                                                                               cTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGAc      >  1:653463/1‑141 (MQ=255)

                                                                                                                   tttAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGcc  <  1:195491/141‑1 (MQ=255)

TTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCC  >  USA300TCH1516_ALE/1744230‑1744485

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A