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 F169 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,750,562	T→C	100%	V197V (GTA→GTG)	betA ←	Oxygen‑dependent choline dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,750,562	0	T	C	100.0%	188.8 / ‑6.5	56	V197V (GTA→GTG)	betA	Oxygen‑dependent choline dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (24/30); minor base A (1/0); total (26/30)
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.

TATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGTACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGTTTTAACTTAA  >  USA300TCH1516_ALE/2750426‑2750698

tataCGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACtt                                                                                                                                      >  1:200370/1‑141 (MQ=255)

 ataCGTAACCCCAGTTGCTTTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTg                                                                                                                                     <  1:335652/141‑1 (MQ=255)

     ttAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTa                                                                                                                                 <  1:377761/140‑1 (MQ=255)

     gTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTa                                                                                                                                 >  2:270457/1‑141 (MQ=255)

          acCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGaa                                                                                                                            >  2:161766/1‑141 (MQ=255)

          acCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGaa                                                                                                                            >  1:318000/1‑141 (MQ=255)

           ccAGTTGCTCTTATACCTTCATATTGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTCAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTTAATCTGACATTTTGCGACCACGATGCACTTGACTATCGAAc                                                                                                                           >  2:330539/1‑141 (MQ=255)

                tGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCGCGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGCCCACGATGCACTTGACTATCGAACGGtac                                                                                                                      >  1:223253/1‑139 (MQ=255)

                tGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTcc                                                                                                                      >  1:159851/1‑141 (MQ=255)

                tGCTCTTCTACCTTCATAATGAATTTCAGTAAAAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTcc                                                                                                                      >  1:331039/1‑141 (MQ=255)

                  ctctTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCaa                                                                                                                    <  1:389564/141‑1 (MQ=255)

                  ctctTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGCTTCAACGGGTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGAACTTCACTATCGAACGGTccca                                                                                                                    >  2:17925/1‑139 (MQ=255)

                    tttctACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCaaaa                                                                                                                  <  1:262667/140‑1 (MQ=255)

                     ttcgtccTTGATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAAc                                                                                                                 <  2:266950/136‑1 (MQ=255)

                      tgtACCTTCACAATGTATTTCCGTTACAAAGACGCGTGTTTCAACGGTTAAGTGTTTACGCTTCATCGCTGGATGTAAATAGGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAAcc                                                                                                                <  2:389477/139‑1 (MQ=255)

                      tctACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAAcc                                                                                                                <  2:343923/141‑1 (MQ=255)

                                   tGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCTATTATGATGGAGTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAAt                                                                                                   >  1:225559/1‑141 (MQ=255)

                                     caTTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATcc                                                                                                 <  1:231101/140‑1 (MQ=255)

                                     aaTTTCATTTACAAAGTCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAACCGGACAGTCGGCTACCACGATGCACGTGACTATCGAACGGTCCAAAACCTACTTGTCTAAATcc                                                                                                 <  2:103698/141‑1 (MQ=255)

                                          cAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTca                                                                                            >  2:100060/1‑141 (MQ=255)

                                           aGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTCAATCCATTcac                                                                                           >  1:309386/1‑141 (MQ=255)

                                             ttACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCAGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTCCTTGTCTACATCCATTCCCAt                                                                                         >  1:339011/1‑141 (MQ=255)

                                               aCAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTCCCTGCTTTCTTTAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCa                                                                                       <  1:90705/141‑1 (MQ=255)

                                                cAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAg                                                                                      <  2:280076/141‑1 (MQ=255)

                                                 aaaGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAgg                                                                                     >  1:158223/1‑141 (MQ=255)

                                                 aaaGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAgg                                                                                     >  2:87117/1‑141 (MQ=255)

                                                        cGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTa                                                                              >  2:205237/1‑141 (MQ=255)

                                                          tgtTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATg                                                                            <  1:82393/141‑1 (MQ=255)

                                                          tgtTTCAACGGTTAAGTTTTTACGCTTCACCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATg                                                                            <  1:625/141‑1 (MQ=255)

                                                            tttCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATAGGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGAt                                                                          <  1:60044/141‑1 (MQ=255)

                                                             ttCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATa                                                                         <  1:5099/141‑1 (MQ=255)

                                                               cAACGGTTAAGTTTGCACGCTCCATCGCTGGATGTAAATATGCTCTTGAAGCTCACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGc                                                                       <  1:303991/141‑1 (MQ=255)

                                                                     ttAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCtt                                                                 >  2:168163/1‑141 (MQ=255)

                                                                       aaGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCa                                                               <  2:244163/141‑1 (MQ=255)

                                                                             ttACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCt                                                         <  2:200370/141‑1 (MQ=255)

                                                                                cGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCa                                                      <  1:100060/141‑1 (MQ=255)

                                                                                cGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCa                                                      >  1:32026/1‑141 (MQ=255)

                                                                                       tcgcgtgATGGACATTTGTTCGTGGAGCTGACATTCGGCGCGCTCGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGGTGGCATGCTTCAACACCTGCATCAAAgg                                               <  2:140052/135‑2 (MQ=255)

                                                                                        cGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGaa                                              <  2:159898/141‑1 (MQ=255)

                                                                                          cTGGATGTAGATATGCTCTAGAAGCCGACATTCGGCGACCGCGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACAGCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATg                                            >  2:203227/1‑141 (MQ=255)

                                                                                              aTGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTg                                        >  1:56643/1‑141 (MQ=255)

                                                                                               tGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTgg                                       <  1:215207/141‑1 (MQ=255)

                                                                                               tGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCCTCACCACCTGCATCAAAGAATGACTgg                                       >  2:276418/1‑141 (MQ=255)

                                                                                                          tctTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGAtt                            <  1:270457/141‑1 (MQ=255)

                                                                                                           ctTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAg                                <  2:209110/136‑1 (MQ=255)

                                                                                                           ctTGAAGCTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAg                                >  1:209110/1‑136 (MQ=255)

                                                                                                                 gCTGACATTCGGCGACCACGATGCACTTGACTATCGAAAGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATCGCCTGCTTCACCACCTGCATCAAAGAATGACTGGAACAAAGGCTTCGTTACt                     >  1:13361/1‑141 (MQ=255)

                                                                                                                  cTGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTg                    >  1:114373/1‑141 (MQ=255)

                                                                                                                   tGACATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTATCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCTACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTgg                   <  2:216224/141‑1 (MQ=255)

                                                                                                                   tGACAGTCGGCGGCCGCGATGCACTTAACTATCGAACGGTCCAAAACCTTCTTGACTAAATCCATTCACATCAGGTGTCTTATGATAGGCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTgg                   <  2:218561/141‑1 (MQ=255)

                                                                                                                      cATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGccc                <  1:258117/141‑1 (MQ=255)

                                                                                                                      cATTCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGccc                <  1:168163/141‑1 (MQ=255)

                                                                                                                         tCGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCg             <  1:372311/141‑1 (MQ=255)

                                                                                                                          cGGCGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCCACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGt            >  1:186953/1‑141 (MQ=255)

                                                                                                                             cGACCACGATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGTATAAAGGATTCGTTGCTGGCCCTCGtttt         >  2:71669/1‑141 (MQ=255)

                                                                                                                                    gATGCACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGTTTTAACTTaa  <  2:309386/141‑1 (MQ=255)

TATACGTAACACCAGTTGCTCTTCTACCTTCATAATGAATTTCAGTTACAAAGGCACGTGTTTCAACGGTTAAGTTTTTACGCTTCATCGCTGGATGTAAATATGCTCTTGAAGCTGACATTCGGCGACCACGATGTACTTGACTATCGAACGGTCCAAAACCTTCTTGTCTAAATCCATTCACATCAGGTGTTTTATGATAGCCTGCTTCAACACCTGCATCAAAGAATGACTGGAATAAAGGATTCGTTGCTGGCCCTCGTTTTAACTTAA  >  USA300TCH1516_ALE/2750426‑2750698

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