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
A7 F74 I1 R1	20	64.4	2271604	93.9%	2133036	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	2,407,399	C→A	intergenic (‑758/‑162)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_tpiA	2,407,399	0	C	A	100.0%	166.0 / NA	50	intergenic (‑758/‑162)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (27/23); total (27/23)

TGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGC  >  NC_000913_3_hsa_tpiA/2407254‑2407543

tGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAatt                                                                                                                                               >  1:159331/1‑149 (MQ=255)

 gAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAatta                                                                                                                                              >  1:132247/1‑149 (MQ=255)

   ggAAATATCATCATCGCGTTTCACTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAattatt                                                                                                                                            >  2:431448/1‑149 (MQ=255)

     aaaTATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTAtttt                                                                                                                                          <  1:448505/149‑1 (MQ=255)

          tcatcatcGCGTTTCATTAGTGCATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCat                                                                                                                                     >  2:389135/1‑149 (MQ=255)

            atcatcGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCatta                                                                                                                                   >  2:190660/1‑149 (MQ=255)

               atcGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCAttatta                                                                                                                                <  1:619730/149‑1 (MQ=255)

                tcGCGTTTCATTAGTTAATTCTTAAATGAGGCATTTTCACGCAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTaa                                                                                                                               <  1:1041037/149‑1 (MQ=255)

                 tgcttttCATTAGTGAATTCTTAAATGAGGCATTTTCAAACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAATAATTCACTACATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAg                                                                                                                              <  2:637917/145‑1 (MQ=255)

                  gcgTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTaatt                                                                                                                             >  1:308779/1‑147 (MQ=255)

                              tGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGcac                                                                                                                 >  1:968547/1‑149 (MQ=255)

                                 aTTCTTAAATGAGGCATTTTCAAACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAAt                                                                                                              <  1:914681/149‑1 (MQ=255)

                                     ttAAATGAGTCATTTTCACACAATTATCTGACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAg                                                                                                          <  1:310900/149‑1 (MQ=255)

                                     ttAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAg                                                                                                          >  1:984811/1‑149 (MQ=255)

                                     ttAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAg                                                                                                          >  2:112203/1‑149 (MQ=255)

                                      tAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACACTTCACTATATAACATTGTATGTCAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGc                                                                                                         >  1:863673/1‑149 (MQ=255)

                                      tAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGc                                                                                                         <  2:159331/149‑1 (MQ=255)

                                                          aaTTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCt                                                                                     <  1:389135/149‑1 (MQ=255)

                                                          aaTTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCt                                                                                     >  2:447578/1‑149 (MQ=255)

                                                            ttATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTa                                                                                   <  1:190660/149‑1 (MQ=255)

                                                            ttATCGTACAGATAAAAAAACCAGACGTACAGTTAAGAATCAGAAAAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGATCCTTCCCCTCTGGCAAAATCTTa                                                                                   <  2:408715/149‑1 (MQ=255)

                                                                    cAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAg                                                                           <  2:968547/149‑1 (MQ=255)

                                                                      gATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATCAACTATAGAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGAc                                                                         <  1:781105/149‑1 (MQ=255)

                                                                         aaaaaaaCCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCtt                                                                      >  1:7225/1‑149 (MQ=255)

                                                                           aaaaaCCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACAACTAATTATTTTGTCATTATTAAGTTATTAAAAGCAGAATAGAGCATTCCCCTCTGGCAAAATCTTATTCTGCAGACTTTCa                                                                    >  2:892620/1‑149 (MQ=255)

                                                                            aaaaCCAGCCTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCaa                                                                   <  1:537218/149‑1 (MQ=255)

                                                                                   gACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATTTTATTTTGCAGACCTTCAAAACACCg                                                            >  1:1042494/1‑149 (MQ=255)

                                                                                     cTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCat                                                                                                                                     >  1:912003/1‑74 (MQ=255)

                                                                                     cTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCat                                                                                                                                     <  2:912003/74‑1 (MQ=255)

                                                                                       tACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGca                                                                                                                  <  2:429827/91‑1 (MQ=255)

                                                                                       tACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGca                                                                                                                  >  1:429827/1‑91 (MQ=255)

                                                                                           aTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTgggg                                                    <  2:132247/149‑1 (MQ=255)

                                                                                           aTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTgggg                                                    <  1:431448/149‑1 (MQ=255)

                                                                                           aTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTgggg                                                    >  2:278574/1‑149 (MQ=255)

                                                                                                      gAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAGAATCTAATTCTGCAGACCTTCAAAACACCGTCCTGGGGGGGTACATTGt                                         >  1:719744/1‑149 (MQ=255)

                                                                                                       aaCAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATCGtt                                        >  2:964310/1‑149 (MQ=255)

                                                                                                       aaCAATTCAATATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGtt                                        <  1:847578/149‑1 (MQ=255)

                                                                                                            ttCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCACAACACCGTCCTGGGGGAGTACATTGTTCTAAg                                   >  2:159186/1‑149 (MQ=255)

                                                                                                            ttCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAg                                   >  1:800610/1‑149 (MQ=255)

                                                                                                             tCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTGCCGTCAGGAAGTAGCTTATTCTGCCGAACTTCAAAACACCGTCCTGAGGGAGTGCATTCTTTTAAGc                                  >  2:123424/1‑149 (MQ=255)

                                                                                                                   tataACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAac                                                                <  2:562652/113‑1 (MQ=255)

                                                                                                                   tataACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAac                                                                >  1:562652/1‑113 (MQ=255)

                                                                                                                   tataACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTTTTCTAAGCTGACtt                            >  1:666992/1‑149 (MQ=255)

                                                                                                                                   aaGCATACACGCCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTgg            <  1:233723/149‑1 (MQ=255)

                                                                                                                                           acacCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACa    <  2:550753/149‑1 (MQ=255)

                                                                                                                                            cacCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTc                                       <  1:484917/113‑1 (MQ=255)

                                                                                                                                            cacCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTc                                       >  2:484917/1‑113 (MQ=255)

                                                                                                                                             acCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGc           <  1:166081/140‑1 (MQ=255)

                                                                                                                                             acCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGc           >  2:166081/1‑140 (MQ=255)

                                                                                                                                             acCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGc  >  2:550504/1‑149 (MQ=255)

TGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGC  >  NC_000913_3_hsa_tpiA/2407254‑2407543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A