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
A10 F28 I1 R1	180	66.5	2263572	99.4%	2249990	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,451,493	T→C	intergenic (‑144/+104)	tynA ← / ← paaZ	copper‑containing amine oxidase/oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,451,493	0	T	C	100.0%	198.4 / NA	56	intergenic (‑144/+104)	tynA/paaZ	copper‑containing amine oxidase/oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (27/29); total (27/29)

GTCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGTGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAATCACCGTGCTGCCTGGCCA  >  NC_000913/1451360‑1451628

gTCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGc                                                                                                                                   >  2:173655/1‑140 (MQ=255)

gTCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGc                                                                                                                                   >  2:362825/1‑140 (MQ=255)

gTCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGc                                                                                                                                   >  1:736619/1‑140 (MQ=255)

gTCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGc                                                                                                                                   >  1:563927/1‑140 (MQ=255)

gTCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGc                                                                                                                                   >  2:716878/1‑140 (MQ=255)

 tCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGcc                                                                                                                                  <  1:104376/140‑1 (MQ=255)

 tCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGcc                                                                                                                                  <  2:419091/140‑1 (MQ=255)

 tCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGcc                                                                                                                                  <  2:602184/140‑1 (MQ=255)

 tCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGcc                                                                                                                                  >  2:646177/1‑140 (MQ=255)

 tCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGcc                                                                                                                                  <  2:654199/140‑1 (MQ=255)

 tCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGcc                                                                                                                                  <  2:746210/140‑1 (MQ=255)

   aGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCt                                                                                                                                <  1:646177/140‑1 (MQ=255)

      tgttgtGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGaa                                                                                                                             <  1:716878/140‑1 (MQ=255)

       gttgtGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGaaa                                                                                                                            >  2:116462/1‑140 (MQ=255)

        ttgtGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGaaaa                                                                                                                           <  1:210055/140‑1 (MQ=255)

        ttgtGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGaaaa                                                                                                                           <  2:961826/140‑1 (MQ=255)

         tgtgTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAAt                                                                                                                          <  2:736619/140‑1 (MQ=255)

          gtgtTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATa                                                                                                                         >  1:961734/1‑140 (MQ=255)

            gtTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGa                                                                                                                       <  1:116462/140‑1 (MQ=255)

                ttGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTa                                                                                                                   <  2:599167/140‑1 (MQ=255)

                ttGTTAGCAACCGCACTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTa                                                                                                                   <  2:694649/140‑1 (MQ=255)

                 tGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTac                                                                                                                  <  2:549062/140‑1 (MQ=255)

                 tGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTac                                                                                                                  <  2:987704/140‑1 (MQ=255)

                  gTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTaca                                                                                                                 <  2:749401/140‑1 (MQ=255)

                     aGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACAcat                                                                                                              <  1:173655/140‑1 (MQ=255)

                     aGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACAcat                                                                                                              <  2:51520/140‑1 (MQ=255)

                            gcgcTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCAt                                                                                                       <  1:362825/140‑1 (MQ=255)

                                  tgtgGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAAtgtg                                                                                                 >  2:743292/1‑140 (MQ=255)

                                    tgGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGAc                                                                                               >  1:478241/1‑140 (MQ=255)

                                    tgGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGAc                                                                                               >  2:484579/1‑140 (MQ=255)

                                              aGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACaa                                                                                     >  1:381758/1‑140 (MQ=255)

                                                     ttCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAg                                                                              >  2:475414/1‑140 (MQ=255)

                                                         caTTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGaa                                                                          >  1:701385/1‑140 (MQ=255)

                                                                   aCTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGc                                                                >  2:350981/1‑140 (MQ=255)

                                                                       aTGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACt                                                            >  1:841976/1‑140 (MQ=255)

                                                                       aTGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACt                                                            >  1:390354/1‑140 (MQ=255)

                                                                       aTGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACt                                                            >  2:54202/1‑140 (MQ=255)

                                                                        tGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCa                                                               >  1:369667/1‑136 (MQ=255)

                                                                        tGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCa                                                               <  2:369667/136‑1 (MQ=255)

                                                                            aaGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCg                                                       >  2:866771/1‑140 (MQ=255)

                                                                                   ttGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGc                                                <  2:563927/140‑1 (MQ=255)

                                                                                   ttGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGc                                                <  2:390354/140‑1 (MQ=255)

                                                                                    tGCCTGCACCCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGc                                                <  2:334056/140‑1 (MQ=255)

                                                                                    tGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGcc                                               <  2:841976/140‑1 (MQ=255)

                                                                                     gCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGccc                                              <  1:54202/140‑1 (MQ=255)

                                                                                      ccTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCt                                             >  1:1065008/1‑140 (MQ=255)

                                                                                           a‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCttcatt                                        >  2:8149/1‑140 (MQ=255)

                                                                                                gCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCAcc                                    >  2:618706/1‑140 (MQ=255)

                                                                                                      ttgttTGGCAGGTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTaa                              <  2:1065008/140‑1 (MQ=255)

                                                                                                                ggTGTGCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAAt                    >  1:147743/1‑140 (MQ=255)

                                                                                                                   gtgCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAATCAc                 >  1:404852/1‑140 (MQ=255)

                                                                                                                    tgCCAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAATCAcc                >  1:737341/1‑140 (MQ=255)

                                                                                                                      ccAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAATCACCGt              <  2:478241/140‑1 (MQ=255)

                                                                                                                       cAGCTTTTCATACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAATCACCGtg             >  1:218640/1‑140 (MQ=255)

                                                                                                                                 tACAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAATCACCGTGCTGCCTGGcc   <  1:907190/140‑1 (MQ=255)

                                                                                                                                  aCAGCGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAATCACCGTGCTGCCTGGcca  <  2:381758/140‑1 (MQ=255)

GTCAGATGTTGTGTTCTTGTTAGCAACCGCGCTCTGTGGGCGGTTTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGGGATTGCCTGCA‑CCTGCCAGGTTGTTTGGCAGGTGTGCCAGCTTTTCATACAGTGGATGCCCTGAAAATAGATGTACACATCATGCATAATGTGACAACGTCACAAAACTTAGTGAAATAAAAGGGCAACTATTCGCCGTTGCCCTTCATTCACCGATTAATCGACAAAATCACCGTGCTGCCTGGCCA  >  NC_000913/1451360‑1451628

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