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
A3 F67 I0 R1	44	83.9	1894234	96.6%	1829830	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,416,458	A→T	100%	I216N (ATT→AAT)	oppD_4 ←	Oligopeptide transport ATP‑binding protein OppD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,416,458	0	A	T	100.0%	160.0 / NA	52	I216N (ATT→AAT)	oppD_4	Oligopeptide transport ATP‑binding protein OppD
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (28/24); total (28/24)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTT  >  USA300TCH1516_ALE/1416321‑1416593

ttttAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGCAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGt                                                                                                                                      >  2:492542/1‑141 (MQ=255)

    aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTCCCCCGTTCAATGCTTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                  <  2:692424/141‑1 (MQ=255)

    aaCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTg                                                                                                                                  <  2:367025/141‑1 (MQ=255)

     aCTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGa                                                                                                                                 >  2:439496/1‑141 (MQ=255)

      cTCAATCATCCTAATTCCTCTTTAATTGTGATCTATATTTAATTCGTCGTGCCGTATACAGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCCATGATTTGACCTTCTTTTAAAACATAATTGTACTGAc                                                                                                                                <  1:190042/141‑1 (MQ=255)

                     cccTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAGAATATTTCAATACAt                                                                                                                 <  1:698143/141‑1 (MQ=255)

                         ctTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACt                                                                                                             >  1:514820/1‑141 (MQ=255)

                            tAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTATAACATAATTGTACTGACAATATTTCAATACATGACTTaa                                                                                                          <  2:437169/141‑1 (MQ=255)

                            tAATTGTGTTCTATATCTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTCCCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTaa                                                                                                          <  2:768013/141‑1 (MQ=255)

                             aaTTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAg                                                                                                         >  1:944344/1‑141 (MQ=255)

                                 gttttCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                     <  1:815518/138‑1 (MQ=255)

                                 gtgtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATTATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACTTGACTTAAGTTAt                                                                                                     >  2:881497/1‑141 (MQ=255)

                                 gtgtTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTAt                                                                                                     >  2:881459/1‑141 (MQ=255)

                                           tctAAGTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGataat                                                                                           <  2:255799/139‑1 (MQ=255)

                                             tAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTCCTGACAATATTTCAATACATGACTTACGTTATGTGTGAtaataa                                                                                         >  2:741513/1‑141 (MQ=255)

                                             tAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGAtaataa                                                                                         >  2:272071/1‑141 (MQ=255)

                                                 tAGACGTTCAGTATACGGATGCAAAGGCTGATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGAAAATATTTCAATACATGACTAAAGTTATGTGTGATAataaataa                                                                                     >  2:427907/1‑141 (MQ=255)

                                                        ttaGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGa                                                                              <  1:753712/139‑1 (MQ=255)

                                                        ccactatgCGGATTCAAATTCTCATACTTGAAAAGATTACTATTATCTTGTTCAATGATTTGACCTTCTCTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAACTAATGTTTGa                                                                              <  2:855444/137‑1 (MQ=255)

                                                         cAGTATACGGATGCAAATGCTCATACTTGAATTGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAc                                                                             <  2:703045/141‑1 (MQ=255)

                                                             ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                         >  1:299602/1‑141 (MQ=255)

                                                             ataCGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATg                                                                         >  1:298246/1‑141 (MQ=255)

                                                                     gCAACTGCTCATACTTGAAATGATTAATATTACCTCGTTCGATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTCACCATGTTCTAATa                                                                 >  1:674353/1‑141 (MQ=255)

                                                                      cAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAc                                                                <  2:707053/141‑1 (MQ=255)

                                                                      cAAATGATCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTTACCTTCTTTTAAAACATAATTGTACTGACAATACTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATAc                                                                <  2:415111/141‑1 (MQ=255)

                                                                        aaTGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACaa                                                              >  1:236550/1‑141 (MQ=255)

                                                                         aTGCTAATACGTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATAGTACTGACAATATTTCACTACATGCCTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAat                                                             <  1:169546/141‑1 (MQ=255)

                                                                             tCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGAACATGTTCTAATACAATATGc                                                         >  2:899063/1‑141 (MQ=255)

                                                                                tACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGt                                                      <  1:439496/141‑1 (MQ=255)

                                                                                tACTTGAAATGATTAAGATTACCTCCTTCAATTATTTGACCTCCTTTTATAACATAATTGTACTGACAATATTTCAATAAATGACTTAAGTTATTTGAGATAAAAAATAATGTTTGAACATGTTCTAATACAATATACTGt                                                      >  2:758747/1‑141 (MQ=255)

                                                                                  cTTGGAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATGGTACTGACAATATTTCAATACATGACTTCAGTTATGTGGGATAATAGATAATGTGTGACCATTTTCTAATACGATGTCCTGtta                                                    >  1:127039/1‑139 (MQ=255)

                                                                                  cTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaa                                                    >  1:591739/1‑141 (MQ=255)

                                                                                    tGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaata                                                  <  2:299602/141‑1 (MQ=255)

                                                                                    tGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaata                                                  <  2:765104/141‑1 (MQ=255)

                                                                                    tGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaata                                                  <  2:599402/141‑1 (MQ=255)

                                                                                    tGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGtaata                                                  <  2:298246/141‑1 (MQ=255)

                                                                                       aaTGATTAATATTACCTCGTCCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAAGAAATAATGTTTGACCATGTTCTAACACAATATGCTGTAATAAAt                                               <  1:517419/141‑1 (MQ=255)

                                                                                                 atTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGCCCATGTTCTATTACAATATGCTTTAATTAATCCATCACtcg                                     >  1:295326/1‑139 (MQ=255)

                                                                                                     ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                                 <  1:930435/141‑1 (MQ=255)

                                                                                                     ccTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAAAATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTa                                 <  1:492542/141‑1 (MQ=255)

                                                                                                      cTCGTTCAATGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTAc                                >  2:319307/1‑141 (MQ=255)

                                                                                                              aTGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCaaa                        >  1:345321/1‑141 (MQ=255)

                                                                                                               tGATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAg                       >  2:157487/1‑141 (MQ=255)

                                                                                                                gATTTGACCTTCTTTTAAAACATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGc                      >  1:476619/1‑141 (MQ=255)

                                                                                                                            ttttAAAACATAATTGTCCTGACAACATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCGAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGc          <  1:260884/141‑1 (MQ=255)

                                                                                                                                 aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTGAAAGCATCGAATGATGCACCTg     >  2:889473/1‑141 (MQ=255)

                                                                                                                                 aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGTTGCAACTg     >  2:575425/1‑141 (MQ=255)

                                                                                                                                 aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTg     >  1:553205/1‑141 (MQ=255)

                                                                                                                                 aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCAAATGATGAAACTg     >  2:419508/1‑141 (MQ=255)

                                                                                                                                 aaaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTACACACACGTTTTGCTGTAATAAATCCATCACTTGCTTACCGTTCAAAGCATCCAATGATGAAACTg     >  1:448473/1‑141 (MQ=255)

                                                                                                                                  aaCATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTgg    <  2:774666/141‑1 (MQ=255)

                                                                                                                                    cATAATTGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGtt  >  1:567792/1‑141 (MQ=255)

TTTTAACTCAATCATAGTAATCCCTCTTTAATTGTGTTCTATATTTAATTAGACGTTCAGTATACGGATGCAAATGCTCATACTTGAAATGATTAATATTACCTCGTTCAATGATTTGACCTTCTTTTAAAACATAAATGTACTGACAATATTTCAATACATGACTTAAGTTATGTGTGATAATAAATAATGTTTGACCATGTTCTAATACAATATGCTGTAATAAATCCATCACTTGATTACCGTTCAAAGCATCCAATGATGCAACTGGTT  >  USA300TCH1516_ALE/1416321‑1416593

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