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
A23 F107 I1 R1	19	39.5	1386814	92.9%	1288350	143.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	2,679,525	G→T	A1074D (GCT→GAT)	yphG ←	DUF4380 domain‑containing TPR repeat protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	2,679,525	0	G	T	97.1%	102.8 / NA	36	A1074D (GCT→GAT)	yphG	DUF4380 domain‑containing TPR repeat protein
Reads supporting (aligned to +/- strand): ref base G (0/1); new base T (21/13); total (21/15)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCA  >  NC_000913_3_pae_tpiA/2679382‑2679665

ggTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGa                                                                                                                                         <  1:494769/149‑1 (MQ=255)

   ttttATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGAttt                                                                                                                                      >  2:308407/1‑148 (MQ=255)

     ttattaACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAAt                                                                                                                                    >  2:110075/1‑149 (MQ=255)

      tattaACGCTGGTTTATTCGAATTATCTGGTGATGAGCGGCTGCGCATGACGCTAACATATGATAGTTTATAGCTTTTAGTGCGCGGGCTTAAAAATAAAAGCCATCACGGTGGTGCATAATGCCGCTTTCGGCCAATCCGGATTAATc                                                                                                                                   <  2:161626/149‑1 (MQ=255)

        ttaACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGc                                                                                                                                 >  2:602477/1‑149 (MQ=255)

                ggCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGCCAAtt                                                                                                                         >  1:642784/1‑149 (MQ=255)

                  tttATTCTAGTTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCa                                                                                                                       <  2:550604/148‑1 (MQ=255)

                     aTTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAgcg                                                                                                                    <  1:67658/149‑1 (MQ=255)

                          aaTTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTCGTGAACGCGGTTAAAAATAAAAGGCATCCCGGTGGTGAATAATGCCGCTTTCTGCCAATCTTGACTAATGGCCGTCCATTCAGCAGGAGc                                                                                                               >  2:367376/1‑149 (MQ=255)

                                       tgaGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTgc                                                                                                  <  1:602477/149‑1 (MQ=255)

                                                 gcgctGCCGCTCAAATATTACACCTCCAGAAGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTccc                                                                                        >  2:670191/5‑149 (MQ=255)

                                                        cGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGGcc                                                                                 >  1:377204/1‑149 (MQ=255)

                                                          cTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGACGGGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCACCGCGAGCGGACTCATATTGCGCAACCTCCCCGAGTCCcg                                                                               >  1:234857/1‑149 (MQ=255)

                                                                tatTACAGTTAATAGGGTTTAGTGAAAGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAACAAACTCAAATTTCGCAACCTCCCCGAGACCCCCGGGCg                                                                         >  2:144125/1‑149 (MQ=255)

                                                                        ttgaTAGGGTGTAGTGAACGCGGGTAAAAATAAAAGGCATCGCGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACGCATATTGCGCAACCTCCCCGAGTCCCCGTGACGCCAGCATc                                                                 >  2:612771/4‑149 (MQ=255)

                                                                            tAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGcca                                                             >  2:589238/1‑149 (MQ=255)

                                                                            tAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCACCATCCcca                                                             >  2:588376/1‑149 (MQ=255)

                                                                             aGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGccac                                                            >  2:259396/1‑149 (MQ=255)

                                                                                              gTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCtt                                           <  2:29643/149‑1 (MQ=255)

                                                                                               ttAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATTCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGTCGGCTTCGCCACCATCAGGCATTTTTCttt                                          <  2:392230/149‑1 (MQ=255)

                                                                                                 aaaaaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAt                                        >  2:617610/1‑149 (MQ=255)

                                                                                                       aaaaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATACGGTCTAAGTGCCGTAAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCACCAGGCATTTTTCTTTATgctgct                                  >  1:164584/1‑149 (MQ=255)

                                                                                                               tCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGa                                                                                     <  1:78051/90‑1 (MQ=255)

                                                                                                               tCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGa                                                                                     >  2:78051/1‑90 (MQ=255)

                                                                                                               tCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGGCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGAATCGCCCCCCTCAGGCCTTTTTCTTTATGCTGCTAGTGTaaa                          >  2:219046/1‑149 (MQ=255)

                                                                                                                 aCGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATc                        <  1:110075/149‑1 (MQ=255)

                                                                                                                       gtgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATa                  >  2:221042/1‑149 (MQ=255)

                                                                                                                        tgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGcc                     >  2:213119/1‑145 (MQ=255)

                                                                                                                        tgAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGcc                     <  1:213119/145‑1 (MQ=255)

                                                                                                                           atggtGCCGCTTTCGGCCAAGCCGGATGAAGCGTGGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCACGAGTCCCGCGGACGCCAGCATCGCCACCAGCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGc              <  2:642715/145‑1 (MQ=255)

                                                                                                                             aatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGa            <  1:126896/149‑1 (MQ=255)

                                                                                                                              atGCCGCTTTCGGCCAACCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCAGCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGac           <  2:164584/149‑1 (MQ=255)

                                                                                                                                     tttCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGt    >  1:459683/1‑149 (MQ=255)

                                                                                                                                     tttCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGt    <  1:221042/149‑1 (MQ=255)

                                                                                                                                     tttCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCATTATGCTGCTGTTGTAAATCGCCTTACACCGACAACAAGt    >  2:421588/1‑149 (MQ=255)

                                                                                                                                       tCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCa  <  2:459683/149‑1 (MQ=255)

GGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCA  >  NC_000913_3_pae_tpiA/2679382‑2679665

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A