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
A21 F63 I0 R1	92	32.2	718920	92.2%	662844	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	478,502	C→A	100%	D342E (GAC→GAA)	ndhF →	NADH dehydrogenase (ubiquinone)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	478,502	0	C	A	100.0%	111.8 / NA	35	D342E (GAC→GAA)	ndhF	NADH dehydrogenase (ubiquinone)
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (15/20); total (15/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGACGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGGAATCA  >  CP000730/478364‑478639

aGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCC‑AAACAAGCATCTGCTAAAGAAGCt                                                                                                                                        >  2:283181/1‑141 (MQ=255)

          gCATTGGGTGTATATTCAGCCGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAAAATTATTTTTACAATCAGGTTCTCTAGTGAAGCGATTCAATATTCCAAAAAAAGAATCTGCTAAAGAAGCTTATGGTTgg                                                                                                                               >  1:172849/1‑141 (MQ=255)

          gCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTgg                                                                                                                               <  1:230354/141‑1 (MQ=255)

               gggTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAGAGAAGCTTATGGCTGGATTGt                                                                                                                          >  1:4489/1‑141 (MQ=255)

                                cGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGCCGTGTATTAg                                                                                                         >  2:220999/1‑141 (MQ=255)

                                  attattCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTTAAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCt                                                                                                       <  1:314951/141‑1 (MQ=255)

                                  attattCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCt                                                                                                       <  1:137240/141‑1 (MQ=255)

                                  attattCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCt                                                                                                       <  1:137245/141‑1 (MQ=255)

                                    tattCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCtat                                                                                                     <  1:234767/141‑1 (MQ=255)

                                     attCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTAGCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCtatt                                                                                                    >  1:219917/1‑141 (MQ=255)

                                        cATTTAATATTGCACGGGATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATc                                                                                                 <  1:175596/141‑1 (MQ=255)

                                                atTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCAtt                                                                                         <  2:330864/141‑1 (MQ=255)

                                                   gCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCt                                                                                      <  2:7346/141‑1 (MQ=255)

                                                   gCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCt                                                                                      <  1:71173/141‑1 (MQ=255)

                                                        gTATGTTTAAAGAAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTAtttt                                                                                 >  1:252966/1‑141 (MQ=255)

                                                          aTTTTTAAAGCAACATTATTTTTTTTTTTTGTTTCTATCGTGAAGCGATTCAATATTCCAAAACAGGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTATCTATTATCGTGGCATTTTTGTTTTgg                                                                               >  2:113864/1‑141 (MQ=255)

                                                            ttttAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGAt                                                                             >  2:154439/1‑141 (MQ=255)

                                                            ttttAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGGATTAGCTATTATCGTGGCATTTCTATTTTGGAt                                                                             >  1:115384/1‑141 (MQ=255)

                                                             tttAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATg                                                                            >  1:135145/1‑141 (MQ=255)

                                                                 aaGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGagta                                                                        <  1:114776/141‑1 (MQ=255)

                                                                     aaCAGTATGTTTAGAATCAGGTCTTATCGTGAAGCGATTCAATATTCCAAAATAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGa                                                                    <  2:38361/141‑1 (MQ=255)

                                                                         ttattTTTACAATCAGGTTCTATCGTCAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTAATTTGGATGAGTAGTGACAGa                                                                <  1:217516/141‑1 (MQ=255)

                                                                            tttttACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGGGTGTTAGCTATTATCGTGGCGTTTCTATTTTGGATGAGTAGTGACAGAAgg                                                             >  1:315329/1‑140 (MQ=255)

                                                                            tttttACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATAGGACGTGTATTAGCTATTATCGTGGCATGTCTATTTTGGAGGAGTAGTGACAGAAgg                                                             >  1:286242/1‑140 (MQ=255)

                                                                               ttACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCa                                                          <  1:205502/141‑1 (MQ=255)

                                                                                   aaTCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATg                                                      <  2:135145/141‑1 (MQ=255)

                                                                                              aTCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGt                                           <  2:150234/141‑1 (MQ=255)

                                                                                                  tGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCAc                                       <  1:220999/141‑1 (MQ=255)

                                                                                                   gAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACt                                      <  1:91980/141‑1 (MQ=255)

                                                                                                          ttCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCAGAATTGTCAAGGGACGTGAATACGCAATTAACGGGGCATTTATCTTTTGGATGAGCAGTGACAAAAGTGCGTATGGAATGTGAAGTGCatttgttggg                               >  2:69203/1‑132 (MQ=255)

                                                                                                              atatTCCAAAAAAAGCATCCGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGCGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGAt                           <  1:195396/141‑1 (MQ=255)

                                                                                                                           aGCATCTGCTAAAGAAGCTTATGGCTGGATTGTTATGGGACGTGTATTAGCTATTATCGTGGGATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGCAGTGTTAAGTGCAGTCATTCTAGGATGGTGATTATTTGt              >  2:129147/1‑141 (MQ=255)

                                                                                                                                cTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATTCAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCtt         <  2:252966/141‑1 (MQ=255)

                                                                                                                                   cTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTCTTAACGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTCCTTGTATCTTGGa      >  1:68795/1‑141 (MQ=255)

                                                                                                                                       aGAAGCTTATGGCTGTATTGTCATGGTACGTGTAGTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTGAGTGCACTCATTCTAGGATGGTCTTTACTTGTATCTTGGAATCa  <  1:217096/141‑1 (MQ=255)

AGTTCAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGACGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTATCTTGGAATCA  >  CP000730/478364‑478639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A