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
A1 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,058,641	(T)_7→8	intergenic (‑231/+25)	serA ← / ← rpiA	phosphoglycerate dehydrogenase/ribose‑5‑phosphate isomerase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,058,634	1	.	T	97.7%	144.7 / ‑3.5	43	intergenic (‑224/+32)	serA/rpiA	phosphoglycerate dehydrogenase/ribose‑5‑phosphate isomerase A
Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (17/25); total (18/25)
Fisher's exact test for biased strand distribution p-value = 4.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

CGTTTGCGTCGCGATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAA‑TTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAACAGTCACCACGCCAGGAATCG  >  NC_000913/3058497‑3058763

cGTTTGCGTCGCGATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAA‑tt                                                                                                                                 >  2:660501/1‑140 (MQ=255)

    tGCGTCGCGATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAA‑tttttt                                                                                                                             >  1:340195/1‑140 (MQ=255)

    tGCGTCGCGATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAA‑tttttt                                                                                                                             >  1:28895/1‑140 (MQ=255)

      cGTCGCGATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACC‑AATTTAATGAAGAGAA‑tttttttta                                                                                                                          >  2:757268/1‑138 (MQ=255)

        tCGCGATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAA‑ttttttttaa                                                                                                                         >  1:455637/1‑137 (MQ=255)

          gcgATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAA‑ttttttttaacg                                                                                                                       >  2:582909/1‑135 (MQ=255)

          gcgATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAA‑ttttttttaacg                                                                                                                       <  1:25477/140‑6 (MQ=255)

           cgATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACgg                                                                                                                       >  1:822755/1‑140 (MQ=255)

             aTGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACgggg                                                                                                                     <  2:822755/140‑1 (MQ=255)

                ttGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAg                                                                                                                  <  2:554254/140‑1 (MQ=255)

                ttGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAg                                                                                                                  <  1:491028/140‑1 (MQ=255)

                ttGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAg                                                                                                                  <  1:582909/140‑1 (MQ=255)

                ttGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAg                                                                                                                  <  2:455637/140‑1 (MQ=255)

                     gAAATATCACGCAAAGGTAATTCTTGGATTAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTcc                                                                                                             <  2:509748/140‑1 (MQ=255)

                       aaTATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGTAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTcccc                                                                                                           <  1:27375/140‑1 (MQ=255)

                        atatCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTcc                                                                                                             >  2:662724/1‑137 (MQ=255)

                        atatCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTcc                                                                                                             <  1:662724/137‑1 (MQ=255)

                          atCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGt                                                                                                        <  1:87306/140‑1 (MQ=255)

                                              ggATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGtt                                                                                    >  1:536730/1‑140 (MQ=255)

                                               gATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGttt                                                                                   >  1:645018/1‑140 (MQ=255)

                                                   aaTATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCAGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGac                                                                               <  2:863439/140‑1 (MQ=255)

                                                         cTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTc                                                                         >  1:396167/1‑140 (MQ=255)

                                                         cTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTc                                                                         <  1:213825/140‑1 (MQ=255)

                                                           ggTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAg                                                                       >  2:157774/1‑140 (MQ=255)

                                                           ggTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAg                                                                       <  2:396167/140‑1 (MQ=255)

                                                            gTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAg                                                                       >  1:453621/1‑139 (MQ=255)

                                                            gTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAg                                                                       <  2:453621/139‑1 (MQ=255)

                                                               tAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGgtgt                                                                   >  1:339132/1‑140 (MQ=255)

                                                                 gagGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGc                                                                 >  1:515531/1‑140 (MQ=255)

                                                                      tttatttaGAGCAATCGACAATTGCCTGGTAAAAGCGAGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATc                                                            >  1:568244/1‑140 (MQ=255)

                                                                            taGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCa                                                      <  2:830770/140‑1 (MQ=255)

                                                                               agCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACg                                                   >  1:726571/1‑140 (MQ=255)

                                                                                 cAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTc                                                 >  1:892841/1‑140 (MQ=255)

                                                                                      gACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCgcgc                                            <  1:165011/140‑1 (MQ=255)

                                                                                      gACAATTGCCTGGTAAAAGCGAGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCgcgc                                            <  2:568244/140‑1 (MQ=255)

                                                                                       aCAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGcc                                           <  2:536730/140‑1 (MQ=255)

                                                                                        cAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCa                                          <  1:660501/140‑1 (MQ=255)

                                                                                                tGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGc                                  >  1:679543/1‑140 (MQ=255)

                                                                                                   tAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCaaa                               <  2:519053/140‑1 (MQ=255)

                                                                                                   tAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCaaa                               <  2:697957/140‑1 (MQ=255)

                                                                                                       aGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAg                           <  2:515531/140‑1 (MQ=255)

                                                                                                       aGCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAg                           <  1:157774/140‑1 (MQ=255)

                                                                                                        gCGTGACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGc                          <  2:726571/140‑1 (MQ=255)

                                                                                                            gACACATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAAc                      >  1:724157/1‑140 (MQ=255)

                                                                                                            gACACATGTCACCAAATTTAATGAAGAGAA‑TTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAACa                     >  2:356846/1‑140 (MQ=255)

                                                                                                             acacATGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAACa                     >  1:305875/1‑140 (MQ=255)

                                                                                                                  tGTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAACGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAACAGTcac                <  2:454619/140‑1 (MQ=255)

                                                                                                                   gTCACCAAATTTAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAACAGTcacc               >  1:654964/1‑140 (MQ=255)

                                                                                                                              tAATGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAACAGTCACCACGCCAGGAAt    <  2:892841/140‑1 (MQ=255)

                                                                                                                                aTGAAGAGAATTTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAACAGTCACCACGCCAGGAATCg  >  1:819097/1‑140 (MQ=255)

CGTTTGCGTCGCGATGTTGAGGAAATATCACGCAAAGGTAATTCTTGGATGAATATGCTGGTTTAGAGGATTTATTTAGAGCAATCGACAATTGCCTGGTAAAAGCGTGACACATGTCACCAAATTTAATGAAGAGAA‑TTTTTTTAACGGGGGAGGTTCCCCCGTCAGATCATTTCACAATGGTTTTGACACCGTCAGGTGTGCCAATCAGCGCAACGTCCGCGCCACGGTTAGCAAACAAGCCAACAGTCACCACGCCAGGAATCG  >  NC_000913/3058497‑3058763

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