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
A9 F28 I1 R1	138	91.1	3071990	99.2%	3047414	138.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,781,054	G→A	intergenic (+37/‑161)	lldD → / → trmL	L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,781,054	0	G	A	100.0%	159.5 / NA	45	intergenic (+37/‑161)	lldD/trmL	L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (14/31); total (14/31)

AATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTG  >  NC_000913/3780920‑3781185

aaTCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCagagagag                                                                                                                                >  1:1016321/1‑140 (MQ=255)

aaTCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCagagagag                                                                                                                                >  2:186673/1‑140 (MQ=255)

  tCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAggg                                                                                                                              <  1:186673/140‑1 (MQ=255)

    gATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGa                                                                                                                            <  2:1410784/140‑1 (MQ=255)

         gCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGtt                                                                                                                       <  1:724490/140‑1 (MQ=255)

             aaTTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGgc                                                                                                                   <  2:993670/140‑1 (MQ=255)

             aaTTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGgc                                                                                                                   <  2:950722/140‑1 (MQ=255)

             aaTTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGgc                                                                                                                   <  1:40260/140‑1 (MQ=255)

             aaTTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTACCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGgc                                                                                                                   <  1:419343/140‑1 (MQ=255)

              aTTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGgcg                                                                                                                  <  2:317086/140‑1 (MQ=255)

              aTTACGCAAGATTCGCTGGTGCA‑GGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGgcgc                                                                                                                 <  2:1184838/140‑1 (MQ=255)

               ttACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGgcgc                                                                                                                 <  2:476768/140‑1 (MQ=255)

               ttACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGgcgc                                                                                                                 <  2:538198/140‑1 (MQ=255)

                tACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCt                                                                                                                <  2:179179/140‑1 (MQ=255)

                 aCGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCtg                                                                                                               <  1:1105080/140‑1 (MQ=255)

                   gCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCtgta                                                                                                             <  1:1169003/140‑1 (MQ=255)

                     aaGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCtgtatg                                                                                                           <  1:566762/140‑1 (MQ=255)

                       gATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCtgtatgta                                                                                                         <  1:1514826/140‑1 (MQ=255)

                        aTTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTAc                                                                                                        >  2:511694/1‑140 (MQ=255)

                                gTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCAc                                                                                                <  1:511694/140‑1 (MQ=255)

                                  gCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCActc                                                                                              <  1:312190/140‑1 (MQ=255)

                                      gggCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGaa                                                                                          >  2:222021/1‑140 (MQ=255)

                                          tGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTATCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGa                                                                                      >  2:583693/1‑140 (MQ=255)

                                            ggTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGaca                                                                                    <  2:96000/140‑1 (MQ=255)

                                                aaGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTATCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGc                                                                                <  1:583693/140‑1 (MQ=255)

                                                 agagTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCa                                                                               <  2:1016321/140‑1 (MQ=255)

                                                 agagTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCa                                                                               <  1:222021/140‑1 (MQ=255)

                                                 agagTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCAATCTGAAACGACACCGCa                                                                               >  2:1366120/1‑140 (MQ=255)

                                                       gCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCttt                                                                         >  2:164966/1‑140 (MQ=255)

                                                       gCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCttt                                                                         >  1:450045/1‑140 (MQ=255)

                                                           gCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCttttttt                                                                     <  2:736099/140‑1 (MQ=255)

                                                               cACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTcc                                                                 <  2:985961/140‑1 (MQ=255)

                                                                  tGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTc                                                              >  2:1070725/1‑140 (MQ=255)

                                                                   ggCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCg                                                             <  1:1366120/140‑1 (MQ=255)

                                                                     cTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGcc                                                           <  2:64536/140‑1 (MQ=255)

                                                                              cGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTc                                                       <  2:989507/135‑1 (MQ=255)

                                                                              cGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTc                                                       >  1:989507/1‑135 (MQ=255)

                                                                              cGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCgggg                                                  >  1:235245/1‑140 (MQ=255)

                                                                                aaaGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGgag                                                <  1:1070725/140‑1 (MQ=255)

                                                                                aaaGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGga                                                 >  2:1158453/1‑139 (MQ=255)

                                                                                aaaGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGga                                                 <  1:1158453/139‑1 (MQ=255)

                                                                                      aaTGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGcc                                          <  1:30524/140‑1 (MQ=255)

                                                                                         gCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCggg                                       <  1:164966/140‑1 (MQ=255)

                                                                                                  tCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGa                              >  1:1269889/1‑140 (MQ=255)

                                                                                                                    ccTACCCCCCCCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACCCCGCACTCTTTTTTTCCCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCAc            <  2:1269889/140‑1 (MQ=39)

                                                                                                                      tAACCCTCTCCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCa          >  1:476702/1‑140 (MQ=255)

                                                                                                                              tcCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg  >  2:615001/1‑140 (MQ=255)

                                                                                                                              tcCCTCAGAGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg  >  1:1070238/1‑140 (MQ=255)

                                                                                                                              cccccCAGAGAGAGGGGCCCGTTCGGCCCTCTATTTACCCCCTCCCCCTGAAACGCCACCGCCCTCTTTTTTTCCCCCTCGCCCCCCGGGGGGGAGGGCGGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg  <  2:1070238/139‑1 (MQ=255)

AATCGATCAGCGAAATTACGCAAGATTCGCTGGTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTG  >  NC_000913/3780920‑3781185

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `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