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
A12 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,724,951	T→C	N123S (AAC→AGC)	glyQ ←	glycine‑‑tRNA ligase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,724,951	0	T	C	100.0%	193.6 / NA	54	N123S (AAC→AGC)	glyQ	glycine‑‑tRNA ligase subunit alpha
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (26/28); total (26/28)

TTCCAGACCGTAGGTGATCTCGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGTTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGATAGTA  >  NC_000913/3724815‑3725081

ttCCAGACCGTAGGTGATCTCGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGcttt                                                                                                                                 <  1:499371/140‑1 (MQ=255)

 tCCAGACCGTAGGTGATCTCGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTc                                                                                                                                >  1:282970/1‑140 (MQ=255)

  ccAGACCGTAGGTGATCTCGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTcc                                                                                                                               <  1:411676/140‑1 (MQ=255)

          tAGGTGATCTCGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATc                                                                                                                       >  1:107727/1‑140 (MQ=255)

              tGATCTCGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTcc                                                                                                                   <  2:44604/140‑1 (MQ=255)

                  ctcGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGa                                                                                                               >  1:838425/1‑140 (MQ=255)

                  ctcGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGa                                                                                                               >  2:98469/1‑140 (MQ=255)

                    cGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGaaa                                                                                                             >  1:391849/1‑140 (MQ=255)

                     gCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAAc                                                                                                            >  1:474681/1‑140 (MQ=255)

                       cGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACgg                                                                                                          >  2:14466/1‑140 (MQ=255)

                       cGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACgg                                                                                                          >  1:170711/1‑140 (MQ=255)

                       cGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACgg                                                                                                          <  1:14466/140‑1 (MQ=255)

                            aCCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTc                                                                                                     >  2:643749/1‑140 (MQ=255)

                                 tttACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGaa                                                                                                >  2:1703/1‑140 (MQ=255)

                                 tttACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGaa                                                                                                <  2:282970/140‑1 (MQ=255)

                                 tttACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGaa                                                                                                <  2:838425/140‑1 (MQ=255)

                                 tttACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGaa                                                                                                <  2:170711/140‑1 (MQ=255)

                                 tttACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGaa                                                                                                <  1:24561/140‑1 (MQ=255)

                                     cacTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGt                                                                                            <  1:1703/140‑1 (MQ=255)

                                      acTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTc                                                                                           <  1:15162/140‑1 (MQ=255)

                                        tCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCgg                                                                                         >  1:387261/1‑140 (MQ=255)

                                            gACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTcc                                                                                     <  1:594966/140‑1 (MQ=255)

                                                  caACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGccc                                                                               <  1:397137/140‑1 (MQ=255)

                                                  caACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGccc                                                                               >  1:473756/1‑140 (MQ=255)

                                                  caACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGccc                                                                               >  1:584923/1‑140 (MQ=255)

                                                    aCCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAg                                                                             <  2:391849/140‑1 (MQ=255)

                                                     ccTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGc                                                                            <  1:656596/140‑1 (MQ=255)

                                                       tgctgGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGctc                                                                          <  1:98469/140‑1 (MQ=255)

                                                         ctgGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCtt                                                                        >  2:31939/1‑140 (MQ=255)

                                                         ctgGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCtt                                                                        >  2:454034/1‑140 (MQ=255)

                                                               gtaagtGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCagag                                                                  <  1:454034/140‑1 (MQ=255)

                                                                 aagtGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGaa                                                                <  2:107727/140‑1 (MQ=255)

                                                                   gtGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAAcc                                                              >  1:350563/1‑140 (MQ=255)

                                                                         tGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTa                                                        <  1:257564/140‑1 (MQ=255)

                                                                          gCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTAc                                                       <  1:848481/140‑1 (MQ=255)

                                                                          gCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTAc                                                       >  1:31539/1‑140 (MQ=255)

                                                                            gTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAg                                                     <  2:325350/140‑1 (MQ=255)

                                                                            gTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAg                                                     <  1:294751/140‑1 (MQ=255)

                                                                                cTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTcc                                                 >  1:46782/1‑140 (MQ=255)

                                                                                  tCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTg                                               >  1:41386/1‑140 (MQ=255)

                                                                                     aTGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAg                                                     <  1:126947/131‑1 (MQ=255)

                                                                                     aTGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAg                                                     >  2:126947/1‑131 (MQ=255)

                                                                                                        cccagcccagTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTa                         >  2:419711/1‑140 (MQ=255)

                                                                                                        cccagcccagTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTa                         >  2:141420/1‑140 (MQ=255)

                                                                                                        cccagcccagTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTa                         >  2:742266/1‑140 (MQ=255)

                                                                                                            gcccagTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGa                     <  1:419711/140‑1 (MQ=255)

                                                                                                                 gTCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAAAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGaccacc                <  2:387261/140‑1 (MQ=255)

                                                                                                                  tCCCCAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCt               >  1:767709/1‑140 (MQ=255)

                                                                                                                   ccccAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTg              <  2:474681/140‑1 (MQ=255)

                                                                                                                     ccAGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGa            <  1:297194/140‑1 (MQ=255)

                                                                                                                       aGGCACCCAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAAc          >  2:389349/1‑140 (MQ=255)

                                                                                                                            cccAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTGCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGAta     >  2:767717/1‑140 (MQ=255)

                                                                                                                             ccAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGAtag    <  2:31539/140‑1 (MQ=255)

                                                                                                                             ccAGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGAtag    <  2:584923/140‑1 (MQ=255)

                                                                                                                               aGCGTCGGGCTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGAtagta  <  2:710452/140‑1 (MQ=255)

TTCCAGACCGTAGGTGATCTCGCCGGTAACCGGTTTACACTCCAGACCACCAACCTGCTGGAAGTAAGTGAACTGCGTCACTTCCATGCCGTTCAGCCACACTTCCCAGCCCAGTCCCCAGGCACCCAGCGTCGGGTTTTCCCAGTTATCTTCCACGAAACGGATGTCGTGAATAGTCGGGTCCATGCCCAGCTCTTTCAGAGAACCGAGGTACAGCTCCTGAATATTGTCCGGCGATGGCTTAATGACCACCTGGAACTGATAGTA  >  NC_000913/3724815‑3725081

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A