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
A19 F57 I1 R1	16	36.0	829726	94.0%	779942	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,373,019	G→A	Q253* (CAG→TAG)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,373,019	0	G	A	100.0%	101.1 / NA	34	Q253* (CAG→TAG)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (11/23); total (11/23)

AATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGTGATG  >  USA300TCH1516_ALE/2372881‑2373155

aagcTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACtata                                                                                                                                        <  2:124536/138‑1 (MQ=255)

  tCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATc                                                                                                                                      <  1:329306/141‑1 (MQ=255)

   cTGAGAACAATGCTCTACCAGCTCTTGGTACTTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGACGTCAATAAATAAGAACGTTAAAGTAGCAATTAAGAGCTATATCg                                                                                                                                     <  2:277137/141‑1 (MQ=255)

   cTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCg                                                                                                                                     <  1:132313/141‑1 (MQ=255)

   cTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCg                                                                                                                                     <  2:403948/141‑1 (MQ=255)

   cTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCg                                                                                                                                     <  1:30826/141‑1 (MQ=255)

   cTGAGAACAATGCACTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCg                                                                                                                                     <  2:82899/141‑1 (MQ=255)

         aCAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTtaata                                                                                                                               >  1:221170/1‑141 (MQ=255)

          cAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTtaataa                                                                                                                              <  2:318121/141‑1 (MQ=255)

          cAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCGACGATTGTACCAGCTGGATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTtaataa                                                                                                                              >  1:289926/1‑141 (MQ=255)

                   aCCAGCTCTTTGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAANAATTAAGAACTATATCGTTAATAATTGACTTgg                                                                                                                     <  1:332423/141‑1 (MQ=255)

                   aCCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAGCAATTAAGAACTATATCGTTAATAATTGACTTgg                                                                                                                     <  2:143348/141‑1 (MQ=255)

                   aCCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTgg                                                                                                                     <  2:204794/141‑1 (MQ=255)

                     cAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGt                                                                                                                   <  1:2027/141‑1 (MQ=255)

                          ctTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTa                                                                                                              >  2:355873/1‑141 (MQ=255)

                              gTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACg                                                                                                          >  1:216368/1‑141 (MQ=255)

                                    tattatCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCaa                                                                                                    <  2:68556/141‑1 (MQ=255)

                                    tattatCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCaa                                                                                                    <  2:359746/141‑1 (MQ=255)

                                    tattatCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCaa                                                                                                    <  1:4677/141‑1 (MQ=255)

                                    tattatCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCaa                                                                                                    <  1:4609/141‑1 (MQ=255)

                                                   taCCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACg                                                                                     <  1:57202/141‑1 (MQ=255)

                                                    aCCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGt                                                                                    >  1:346605/1‑141 (MQ=255)

                                                                aGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACt                                                                        <  2:175290/141‑1 (MQ=255)

                                                                       gCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATc                                                                 <  2:253178/141‑1 (MQ=255)

                                                                       gCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATc                                                                 <  2:182460/141‑1 (MQ=255)

                                                                                       cTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATNTTACCCACAATACCAg                                                 <  1:355873/141‑1 (MQ=255)

                                                                                                     tCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGaatc                                   >  2:248105/1‑141 (MQ=255)

                                                                                                     tCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGaatc                                   >  1:71197/1‑141 (MQ=255)

                                                                                                     tCAATAAATAAGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGaatc                                   >  2:160260/1‑141 (MQ=255)

                                                                                                        ataaataaGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGaatcaat                                >  1:14710/1‑141 (MQ=255)

                                                                                                        ataaataaGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGaatcaat                                >  1:130594/1‑141 (MQ=255)

                                                                                                        ataaataaGAACGTTAAAATAACAATTAAGAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGaatcaat                                >  1:183290/1‑141 (MQ=255)

                                                                                                                                     gAACTATATCGTTAATACTTGACTTGTGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGtgat   <  2:289926/141‑1 (MQ=255)

                                                                                                                                     gAACTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGtgat   <  2:216368/141‑1 (MQ=255)

                                                                                                                                      aaCTATATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGCTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGtgatg  <  2:31404/141‑1 (MQ=255)

AATCTGAGAACAATGCTCTACCAGCTCTTGGTAATTTATTATCTTTCATAATACCTGCTTGAGTAGCAACAGCTACTAATGTACCAGCTGTATCAAAGAAATCAATAAATAAGAACGTTAAAATAACAATTAAGAACTGTATCGTTAATAATTGACTTGGGTCTTTAAACGCTTCAAATGCAGCACCGAACGTTGGTTCAATACTTGGAATCTTACCCACAATACCAGATGGCATTTGAATCAATCCAGTGAACATACCAACGATTGCTGTGATG  >  USA300TCH1516_ALE/2372881‑2373155

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

GATK/CNVnator alignment

N/A