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 F1 I2 R1	78	48.0	2243616	94.8%	2126947	114.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,512,258	(T)_5→6	coding (449/1239 nt)	mntH ←	manganese/divalent cation transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,512,253	1	.	T	100.0%	122.2 / NA	36	P152T (CCG→ACG)	mntH	manganese/divalent cation transporter
Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (18/18); total (18/18)

ACCGCTTCCGAAGTAGGTAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGG‑TTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCA  >  NC_000913/2512117‑2512378

aCCGCTTCCGAAGTAGGTAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGG‑tt                                                                                                                             >  1:135771/1‑139 (MQ=255)

          aaGTAGGTAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCcgc                                                                                                                    >  2:544643/1‑139 (MQ=255)

                 tAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                             <  2:135771/139‑1 (MQ=255)

                 tAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                             <  1:544643/139‑1 (MQ=255)

                   aaCTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTATGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTgta                                                                                                           <  1:671503/139‑3 (MQ=255)

                           aTCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAACCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTaaa                                                                                                   <  1:789865/139‑1 (MQ=255)

                                        tACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTcg                                                                                      >  2:398689/1‑139 (MQ=255)

                                             aGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTaa                                                                                                    <  2:17829/120‑1 (MQ=255)

                                             aGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTaa                                                                                                    >  1:17829/1‑120 (MQ=255)

                                             aGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATc                                                                                 <  2:672717/139‑1 (MQ=255)

                                                       ggTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCa                                                                       >  2:419768/1‑139 (MQ=255)

                                                         ttAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCAcc                                                                     >  2:678120/1‑139 (MQ=255)

                                                          tAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACcg                                                                    <  2:652881/139‑1 (MQ=255)

                                                            ggCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACcgcg                                                                  <  1:519827/139‑1 (MQ=255)

                                                                          cAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGa                                                    <  1:129884/139‑1 (MQ=255)

                                                                             cTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAac                                                 >  2:453327/1‑139 (MQ=255)

                                                                               cGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGcaa                                                          >  1:632661/1‑128 (MQ=255)

                                                                               cGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGcaa                                                          <  2:632661/128‑1 (MQ=255)

                                                                                gACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                             <  2:825525/76‑1 (MQ=255)

                                                                                gACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTg                                                                                                             >  1:825525/1‑76 (MQ=255)

                                                                                      gTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAAt                                        <  1:638079/139‑1 (MQ=255)

                                                                                      gTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAAt                                        <  1:398689/139‑1 (MQ=255)

                                                                                              cgGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTaa                                >  2:715450/1‑139 (MQ=255)

                                                                                               ggCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGa                                                    <  2:935600/118‑1 (MQ=255)

                                                                                               ggCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGa                                                    >  1:935600/1‑118 (MQ=255)

                                                                                               ggCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTaaa                               >  1:240434/1‑139 (MQ=255)

                                                                                                gCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTaaaa                              >  2:177113/1‑139 (MQ=255)

                                                                                                          acaGTAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATcgccg                    <  1:453327/139‑1 (MQ=255)

                                                                                                              tAACCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCAcc                >  1:48633/1‑139 (MQ=255)

                                                                                                                aCCCGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCaa              >  1:832427/1‑139 (MQ=255)

                                                                                                                   cGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCAcc                                                                     >  2:537229/1‑81 (MQ=255)

                                                                                                                   cGCCAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCAcc                                                                     <  1:537229/81‑1 (MQ=255)

                                                                                                                     ccAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAAt         >  2:556339/1‑139 (MQ=255)

                                                                                                                     ccAATCACTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAAt         >  1:392984/1‑139 (MQ=255)

                                                                                                                            cTTTCTCCAGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCa  <  2:516496/139‑1 (MQ=255)

                                                                                                                                    aGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACcgcg                                                                  <  2:144173/67‑1 (MQ=255)

                                                                                                                                    aGCGGTTTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACcgcg                                                                  >  1:144173/1‑67 (MQ=255)

ACCGCTTCCGAAGTAGGTAAACTCGGGATCACCATTCCTTTACCCAGCTGCGCCAGGTTAGGCTGGGAGAAAATCAACTCGACAATGTAAGCCGCGGCAACAAACAACAGTAACCCGCCAATCACTTTCTCCAGCGG‑TTTTTGCCCGCGACGTTGCAGCATTAAAATCAGGAAAGTCGCGATCCCCGTCAGCACCGCGCCCTGCAACAACGAAACACCAAGAATGAGTTTAAAACCGATCGCCGCACCAATAAATTCCGCCA  >  NC_000913/2512117‑2512378

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A