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	123	51.0	1731148	99.3%	1719029	138.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,667,698	A→G	intergenic (‑118/+93)	gadA ← / ← ccp	glutamate decarboxylase A/cytochrome c peroxidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,667,698	0	A	G	100.0%	174.2 / NA	47	intergenic (‑118/+93)	gadA/ccp	glutamate decarboxylase A/cytochrome c peroxidase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (21/26); total (21/26)

ACAGCTTCTGGTCCATTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTATAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACGGCGTGTACACCCCGTTCAGA  >  NC_000913/3667565‑3667833

aCAGCTTCTGGTCCATTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTtgtaatat                                                                                                                                   <  2:135923/140‑1 (MQ=255)

 cAGCTTCTGGTCCATTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTtgtaatata                                                                                                                                  <  2:216904/140‑1 (MQ=255)

 cAGCTTCTGGTCCATTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTtgtaatata                                                                                                                                  <  2:174643/140‑1 (MQ=255)

      tCTGGTCCATTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACAt                                                                                                                             >  1:125268/1‑140 (MQ=255)

          gTCCATTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTaa                                                                                                                         >  2:770563/1‑140 (MQ=255)

            ccATTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACa                                                                                                                       >  1:398169/1‑140 (MQ=255)

              aTTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATg                                                                                                                     >  2:607884/1‑140 (MQ=255)

              aTTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATg                                                                                                                     >  2:359797/1‑140 (MQ=255)

               tttCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGa                                                                                                                    >  1:93563/1‑140 (MQ=255)

                 tCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGata                                                                                                                  <  2:68764/140‑1 (MQ=255)

                                         ggCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATc                                                                                          <  1:158365/140‑1 (MQ=255)

                                                     gTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATc                                                                              >  2:63765/1‑140 (MQ=255)

                                                                   cAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCt                                                                >  1:110567/1‑140 (MQ=255)

                                                                    aaTGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTg                                                               >  1:453019/1‑140 (MQ=255)

                                                                       ggAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTc                                                            <  2:824458/140‑1 (MQ=255)

                                                                          aGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCggg                                                         <  2:453019/140‑1 (MQ=255)

                                                                              aGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGAt                                                     >  1:850809/1‑140 (MQ=255)

                                                                                gCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCa                                                   >  1:832061/1‑140 (MQ=255)

                                                                                 cATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCaa                                                  >  1:188739/1‑140 (MQ=255)

                                                                                  aTTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATc                                                    <  1:24651/137‑1 (MQ=255)

                                                                                  aTTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATc                                                    >  2:24651/1‑137 (MQ=255)

                                                                                   ttACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAaat                                                <  1:9022/140‑1 (MQ=255)

                                                                                    tACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAaatt                                               >  2:588682/1‑140 (MQ=255)

                                                                                          cTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAattat                                         >  2:463544/1‑140 (MQ=255)

                                                                                          cTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAattat                                         <  2:398169/140‑1 (MQ=255)

                                                                                           ttAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAattatt                                        >  1:250898/1‑140 (MQ=255)

                                                                                           ttAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAattatt                                        >  2:611678/1‑140 (MQ=255)

                                                                                            tAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTg                                       >  2:476271/1‑140 (MQ=255)

                                                                                             aaTTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGt                                      <  1:588682/140‑1 (MQ=255)

                                                                                              aTTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGt                                      >  1:683999/1‑139 (MQ=255)

                                                                                              aTTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGt                                      <  2:683999/139‑1 (MQ=255)

                                                                                                 tAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTAt                                  <  1:359797/140‑1 (MQ=255)

                                                                                                 tAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTAt                                  <  2:832061/140‑1 (MQ=255)

                                                                                                 tAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTAt                                  <  1:607884/140‑1 (MQ=255)

                                                                                                 tAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACCTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTAt                                  <  1:805851/140‑1 (MQ=255)

                                                                                                   aaTAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATcc                                <  1:463544/140‑1 (MQ=255)

                                                                                                   aaTAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATcc                                <  1:63765/140‑1 (MQ=255)

                                                                                                     tAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTg                              <  2:188739/140‑1 (MQ=255)

                                                                                                     tAACAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTg                              <  1:468016/140‑1 (MQ=255)

                                                                                                        cAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGttt                                    <  2:685290/131‑1 (MQ=255)

                                                                                                        cAAAATCCTAAGCAGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGttt                                    >  1:685290/1‑131 (MQ=255)

                                                                                                                     aGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACgg                     <  1:262952/133‑1 (MQ=255)

                                                                                                                     aGAAAAACGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACgg                     >  2:262952/1‑133 (MQ=255)

                                                                                                                       aaaaaCGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTACATATACGGCGTGTacac            <  2:457962/140‑1 (MQ=255)

                                                                                                                         aaaCGACTTTTTGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACGGCGTGTACAccc          <  2:93563/140‑1 (MQ=255)

                                                                                                                                 ttttGTAATATAAACATTTAACATGATAATGTTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACGGCGTGTACACCCCGTTCAGa  <  1:770563/140‑1 (MQ=255)

                                                                                                                                 ttttGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACGGCGTGTACACCCCGTTCAGa  <  2:125268/140‑1 (MQ=255)

                                                                                                                                 ttttGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACGGCGTGTACACCCCGTTCAGa  <  2:110567/140‑1 (MQ=255)

                                                                                                                                 ttttGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACGGCGTGTACACCCCGTTCAGa  <  1:48014/140‑1 (MQ=255)

                                                                                                                                 ttttGTAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACGGCGTGTACACCCCGTTCAGa  <  1:391390/140‑1 (MQ=255)

ACAGCTTCTGGTCCATTTCGAACTCCTTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTATCCGCAATGGAAGCAAGGCATTACAGGCTTAATTTAAATAACAAAATCCTAAGCAGAAAAACGACTTTTTATAATATAAACATTTAACATGATAATATTAAAAACAGACTTTATTATCGTAATAAAAATCGCCCAAACATTGCTGTTCGGGCGATCAAATTAATTATTGTTTATCCTGCATATACGGCGTGTACACCCCGTTCAGA  >  NC_000913/3667565‑3667833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A