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	1,761,889	C→A	100%	D388Y (GAT→TAT)	fpgS ←	Folylpolyglutamate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,761,889	0	C	A	100.0%	174.1 / ‑6.5	55	D388Y (GAT→TAT)	fpgS	Folylpolyglutamate synthase
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (31/23); minor base T (1/0); total (32/23)
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.

TTCATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGGTT  >  USA300TCH1516_ALE/1761755‑1762023

ttcATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTaa                                                                                                                                  >  1:553810/1‑141 (MQ=255)

ttcATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTaa                                                                                                                                  >  1:269842/1‑141 (MQ=255)

ttcATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTACACGTAGCCCTctactca                                                                                                                                  >  1:648669/1‑139 (MQ=255)

ttcATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAAGACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTaa                                                                                                                                  >  1:588835/1‑141 (MQ=255)

    tGGCTATTTTAGTTTTAGTTTTATAATGCTTCAATGTCTAATTTTGGTTTAACTTCACTTATGAAATACACACTACCGGTGATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTTACCATATACTCATTGt                                                                                                                              >  2:200595/1‑141 (MQ=255)

    tGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCATCGTAGTCATATACTAATTGt                                                                                                                              >  2:607249/1‑141 (MQ=255)

            tttgagttagttttaTAATGCTTCAAAGACTAATTTAGAGTTAACTTAACTAATGAAAAATAGAATACAGGTAATTAATAATGTATCACCTGCATAATTTTTGATAAATTCAAAGTAGTAATAAACTAATTGTTTTttatt                                                                                                                      >  2:214540/7‑140 (MQ=255)

            ttagttttagttTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTtcatc                                                                                                                      >  2:150456/1‑141 (MQ=255)

             tagttttagtttTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGGCTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTtcatct                                                                                                                     >  1:427677/1‑140 (MQ=255)

                        ttaTAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAAtact                                                                                                          <  2:242293/141‑1 (MQ=255)

                        ttaTAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAAtact                                                                                                          <  1:498922/141‑1 (MQ=255)

                           taaatcgtCAAACTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActacc                                                                                                       <  2:627151/134‑1 (MQ=255)

                           taATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActacc                                                                                                       <  1:119162/141‑1 (MQ=255)

                           taATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActacc                                                                                                       <  1:211037/141‑1 (MQ=255)

                           taATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTACGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActacc                                                                                                       <  2:180105/141‑1 (MQ=255)

                           aaaTGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATActacc                                                                                                       <  2:99099/140‑1 (MQ=255)

                                      aGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATttctt                                                                                            >  2:271088/1‑141 (MQ=255)

                                        cctcaTTGTGATTTACCTTCACTTCTGAAATACAGACTACCGGTAATTACTAATGTATAACCTTGATAATTTTTTATAAATTTAAAGTAGTCATATACTAATTNTATTTCATCATTTTCAATACTTCCTACAATTtctgct                                                                                          >  2:81362/5‑141 (MQ=255)

                                         cTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTattctt                                                                                         >  2:15097/1‑141 (MQ=255)

                                          tAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCttt                                                                                        >  1:244262/1‑141 (MQ=255)

                                                ttaTTTTACTTCACATATAAAATATAGAATAACGGTAATTATTAATGTATCAACTTGATAATTTTTTATAAATTCAACGGAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTaa                                                                                  <  1:53608/139‑1 (MQ=255)

                                                tGATTTATCTTCACTTATGAAATACAGACTACCGGTTATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTaa                                                                                  <  2:35262/141‑1 (MQ=255)

                                                   tttAACTTCACTTATGAAATACAGACTACCGGTAATTACTAGTGTTTCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGc                                                                               >  1:130528/1‑141 (MQ=255)

                                                   tttAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAGCGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGc                                                                               >  1:21624/1‑141 (MQ=255)

                                                   tttAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGc                                                                               >  1:466003/1‑141 (MQ=255)

                                                        cgtCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGACAATTTTTTATAAATTCAACGTAGTCATATACTAATCGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCg                                                                          >  2:491940/3‑141 (MQ=255)

                                                        cTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTCATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCg                                                                          <  1:258507/141‑1 (MQ=255)

                                                        cTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCg                                                                          <  1:617030/141‑1 (MQ=255)

                                                           cACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGaa                                                                       <  2:485108/141‑1 (MQ=255)

                                                            aCTTATGAAATACAGCCTACCGGTAATTAATAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTATCTACAATTTCTTCTTTGCGTAAGGCTTTCGGaaa                                                                      >  2:390864/1‑141 (MQ=255)

                                                            aCTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGaaa                                                                      >  2:586030/1‑141 (MQ=255)

                                                                 tGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCTTAACGGTTTCGGTAAATCaa                                                                 >  1:220551/1‑141 (MQ=255)

                                                                         aGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTTTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGtt                                                         >  1:135203/1‑141 (MQ=255)

                                                                         aGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGtt                                                         >  1:100904/1‑141 (MQ=255)

                                                                                  ggaaTCACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTCCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAAc                                                <  1:81362/139‑1 (MQ=255)

                                                                                  gTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAAc                                                <  2:272436/141‑1 (MQ=255)

                                                                                  gTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAAc                                                <  2:459406/141‑1 (MQ=255)

                                                                                  gTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAAc                                                <  2:217424/141‑1 (MQ=255)

                                                                                     aTTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTa                                             <  1:271088/141‑1 (MQ=255)

                                                                                      ttACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTAt                                            <  1:604336/141‑1 (MQ=255)

                                                                                         cTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATgcg                                         >  2:265473/1‑141 (MQ=255)

                                                                                         cTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATgcg                                         >  2:145963/1‑141 (MQ=255)

                                                                                         cTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATgcg                                         <  1:95136/141‑1 (MQ=255)

                                                                                         cTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATgcg                                         >  2:596745/1‑141 (MQ=255)

                                                                                           aaTGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCa                                       >  2:327499/1‑141 (MQ=255)

                                                                                                    ccTTGATAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACtt                              <  1:518486/141‑1 (MQ=255)

                                                                                                         aTAATTTTTTATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAAtt                         >  1:393814/1‑140 (MQ=255)

                                                                                                            aTTTTTTATAAATTCAACGTAAAAGTTTATGGATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGttt                      >  2:471857/1‑141 (MQ=255)

                                                                                                             ttttttATAAATTCCACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTg                     >  1:356748/1‑141 (MQ=255)

                                                                                                             ttttttATAAATTCAACGTAGTCATATCTTATTTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTg                     <  2:666789/141‑1 (MQ=255)

                                                                                                              tttttATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGa                    >  2:7633/1‑141 (MQ=255)

                                                                                                              tttttATAAATTCAACGTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGa                    >  2:648337/1‑141 (MQ=255)

                                                                                                                          aaaCGTAGTCATATACTAATTTTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTaa        <  2:480025/140‑1 (MQ=255)

                                                                                                                              gTAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATcag    >  2:400994/1‑139 (MQ=255)

                                                                                                                               tAGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGG‑AAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGGtt  <  1:419592/141‑1 (MQ=255)

                                                                                                                                aGTCATATACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGGtt  >  1:165959/1‑141 (MQ=255)

TTCATGGCTATTTTAGTTTTAGTTTTATAATGCTTCAAAGTCTAATTTTGATTTAACTTCACTTATGAAATACAGACTACCGGTAATTACTAATGTATCACCTTGATAATTTTTTATAAATTCAACGTAGTCATCTACTAATTGTATTTCATCATTTTCAATACTACCTACAATTTCTTCTTTGCGTAACGCTTTCGGAAAATCAAATTCAGTTGCATAAAACGTATGCGCAATTAAACTTAAATGTTTGACCATCTCGTTAATCGGTT  >  USA300TCH1516_ALE/1761755‑1762023

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