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	106	58.2	1336546	90.2%	1205564	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,298,108	T→A	100%	intergenic (+4/‑232)	pnp → / → USA300HOU_1207	polyribonucleotide nucleotidyltransferase/beta‑lactamase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,298,108	0	T	A	100.0%	107.8 / ‑6.5	37	intergenic (+4/‑232)	pnp/USA300HOU_1207	polyribonucleotide nucleotidyltransferase/beta‑lactamase
Reads supporting (aligned to +/- strand): ref base T (0/1); major base A (17/18); minor base G (1/0); total (18/19)
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.

TTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTAT  >  CP000730/1297972‑1298238

ttCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGATACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATaaa                                                                                                                                >  1:473706/1‑141 (MQ=255)

ttCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGATACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATaaa                                                                                                                                >  1:473872/1‑141 (MQ=255)

          tCAAAAAATAGAATCGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgac                                                                                                                      >  1:608632/1‑141 (MQ=255)

            aaaaaaTAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgacga                                                                                                                    <  1:401312/141‑1 (MQ=255)

            aaaaaaTAAAATTGAAAAAGTGGAAGATGTATTAAAAAGCGGTAACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAAGTCGATGAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATgacga                                                                                                                    <  2:68412/141‑1 (MQ=255)

              aaaaTAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATGGATAAACAAGATCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATGTAAAGTACTATGACGACa                                                                                                                  >  2:345432/1‑141 (MQ=255)

                 aTAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATg                                                                                                               <  1:479356/141‑1 (MQ=255)

                 aTAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATg                                                                                                               <  1:394992/141‑1 (MQ=255)

                      aTTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGATAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAAAAGAATAATATATAAAGTCATCTGACAACAATGTATCg                                                                                                          >  2:319835/1‑141 (MQ=255)

                           aaaaGTGGAAGATGTATTAAAAATCGGTGACACAATTGAACTTAAGACTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCAtg                                                                                                     >  2:432254/1‑141 (MQ=255)

                                 ggAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGAttt                                                                                               >  1:51176/1‑141 (MQ=255)

                                           ttAAAAATCGGTGACAAAATTAAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCa                                                                                     >  1:341913/1‑141 (MQ=255)

                                             aaaaaTCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACt                                                                                   <  2:661483/141‑1 (MQ=255)

                                             aaaaaTCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACt                                                                                   <  2:131621/141‑1 (MQ=255)

                                               aaaTCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACttt                                                                                 <  2:87551/141‑1 (MQ=255)

                                                   cGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATTCCACTTTTTAc                                                                             >  2:614829/1‑141 (MQ=255)

                                                    ggTGACACAATTAAAGTTAAGATTACTGAAAATGATAAACAAGGTCGAGTAAAAGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACg                                                                            >  2:640831/1‑141 (MQ=255)

                                                     gTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGa                                                                           >  2:499024/1‑141 (MQ=255)

                                                       gACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAg                                                                         >  2:352184/1‑141 (MQ=255)

                                                               tGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGt                                                                 <  2:51176/141‑1 (MQ=255)

                                                                 aaGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGttt                                                               <  1:174495/141‑1 (MQ=255)

                                                                                  aTTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGa                                              <  1:583927/141‑1 (MQ=255)

                                                                                         aaCAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACAtttt                                       <  1:587699/141‑1 (MQ=255)

                                                                                             aGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTaaaa                                   <  1:499024/141‑1 (MQ=255)

                                                                                              ggTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAAc                                  >  2:449216/1‑141 (MQ=255)

                                                                                                tCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTGTTGAATTTGTTGTATTGAACATTTTAAAACGc                                >  1:445604/1‑141 (MQ=255)

                                                                                                      aaaTGCTTCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTttatt                          <  2:341913/141‑1 (MQ=255)

                                                                                                            ttCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTtg                    <  1:510936/141‑1 (MQ=255)

                                                                                                            ttCACATAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTtg                    >  1:363836/1‑141 (MQ=255)

                                                                                                              cacaTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTtgtg                  >  1:35383/1‑141 (MQ=255)

                                                                                                                 aTAGAGCATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGc               >  1:200047/1‑141 (MQ=255)

                                                                                                                       cATTAGAAGAATAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACCCTTTATTATTTTTTTTGTAACTGt         >  2:580834/1‑141 (MQ=255)

                                                                                                                        aTTAGAAGAATAATATATAAAGGCATATGACGACAATGTATCGTCATGTGATTTTTTTAGGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAGCGCTTTATTATTTTGTGTGCAACTGtt        <  2:248674/141‑1 (MQ=255)

                                                                                                                          tAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTaa      <  2:505303/141‑1 (MQ=255)

                                                                                                                           aggagaaTAATATATAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAAt     <  1:215580/138‑1 (MQ=255)

                                                                                                                              ataataatATAAAAAGTCATAGGACGACAATGTATCGTCATGTGACTTTTTTATGCCACTTTTTACGAAGTCACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTAt  <  2:18808/139‑1 (MQ=255)

                                                                                                                              agaaTAATATATAACGTCATATGACGATAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTAt  <  2:498911/141‑1 (MQ=255)

TTCACAAATTTCAAAAAATAGAATTGAAAAAGTGGAAGATGTATTAAAAATCGGTGACACAATTGAAGTTAAGATTACTGAAATTGATAAACAAGGTCGAGTAAATGCTTCACATAGAGCATTAGAAGAATAATATTTAAAGTCATATGACGACAATGTATCGTCATGTGATTTTTTTATGCCACTTTTTACGAAGTGACCCGTTTTGAATTTGTTGTATTGAACATTTTAAAACGCTTTATTATTTTGTGTGCAACTGTTAATTAT  >  CP000730/1297972‑1298238

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