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 I1 R1	759	71.0	3673240	91.5%	3361014	104.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,252,038	G→A	A325T (GCT→ACT)	dhaR →	dhaKLM operon transcription activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,252,038	0	G	A	100.0%	118.7 / NA	38	A325T (GCT→ACT)	dhaR	dhaKLM operon transcription activator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (21/17); total (21/17)

TTGATGCGGTGATAACCCTTAAACCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCGCTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTTGTGGAGAAGAGGGCGTGGGCAAGGCAC  >  NC_000913/1251910‑1252152

ttGATGCGGTGATAACCCTTAAACCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCGGCCATACCTTCACTCATATGcc                                                                                                          >  2:630373/1‑139 (MQ=255)

    tGCGGTGATAACCCTTAAACCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAg                                                                                                      >  2:568398/1‑139 (MQ=255)

      cGGTGATAACCCTTAAACCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGa                                                                                                    >  1:598344/1‑139 (MQ=255)

        gTGATAACCCTTAAACCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACg                                                                                                  >  2:1051934/1‑139 (MQ=255)

           aTAACCCTTAAACCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATc                                                                                               <  2:370307/139‑1 (MQ=255)

              aCCCTTAAACCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGc                                                                                            <  2:561686/139‑1 (MQ=255)

                     aaCCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACccg                                                                                     <  1:1623974/139‑1 (MQ=255)

                         gATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCcgccgc                                                                                 <  2:598344/139‑1 (MQ=255)

                          ataataGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCt                                                                                >  2:426976/1‑139 (MQ=255)

                                    cGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCt                                                                                <  1:703400/129‑1 (MQ=255)

                                    cGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCt                                                                                >  2:703400/1‑129 (MQ=255)

                                     gCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCcgccgc                                                                                 >  1:851784/1‑127 (MQ=255)

                                     gCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCcgccgc                                                                                 <  2:851784/127‑1 (MQ=255)

                                       aGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTgg                                                                   <  1:1423780/139‑1 (MQ=255)

                                            aCCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGa                                                                             >  1:1308195/1‑124 (MQ=255)

                                            aCCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGa                                                                             <  2:1308195/124‑1 (MQ=255)

                                              cAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACg                                                                                                  >  2:1388318/1‑101 (MQ=255)

                                              cAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACg                                                                                                  <  1:1388318/101‑1 (MQ=255)

                                                 cTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAggcg                                                         <  1:1051934/139‑1 (MQ=255)

                                                 cTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAggcg                                                         <  1:630373/139‑1 (MQ=255)

                                                       tttGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGgcgcgc                                                   <  1:568398/139‑1 (MQ=255)

                                                           ttgCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACg                                                                                                  >  1:1544284/1‑88 (MQ=255)

                                                           ttgCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACg                                                                                                  <  2:1544284/88‑1 (MQ=255)

                                                                             cAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCcgccgc                                                                                 >  2:777146/1‑87 (MQ=255)

                                                                             cAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCcgccgc                                                                                 <  1:777146/87‑1 (MQ=255)

                                                                             cAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCttt                             >  2:230056/1‑139 (MQ=255)

                                                                             cAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCttt                             >  2:419015/1‑139 (MQ=255)

                                                                               gATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTtgt                           >  2:1297291/1‑139 (MQ=255)

                                                                                     gCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTTGTGGagaa                     >  2:1465866/1‑139 (MQ=255)

                                                                                         ttGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTTGTGGAGAAGAgg                 >  1:814672/1‑139 (MQ=255)

                                                                                          tgatgaCCAGTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTTGTGGAGAAGAggg                >  1:1370550/1‑139 (MQ=255)

                                                                                                   gTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATg                                                                                                            <  2:1217333/38‑1 (MQ=255)

                                                                                                   gTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATg                                                                                                            >  1:1217333/1‑38 (MQ=255)

                                                                                                   gTCAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTTGTGGAGAAGAGGGCGTGGGCaa       >  1:63410/1‑139 (MQ=255)

                                                                                                     cAATTAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTTGTGGAGAAGAGGGCGTGGGCAAgg     <  2:1014138/139‑1 (MQ=255)

                                                                                                        ttAGGAAAAGTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTTGTGGAGAAGAGGGCGTGGGCAAGGCAc  >  2:1775361/1‑139 (MQ=255)

                                                                                                                 gTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGgcgcgc                                                   >  2:378412/1‑81 (MQ=255)

                                                                                                                 gTCAGCCATACCTTCACTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGgcgcgc                                                   <  1:378412/81‑1 (MQ=255)

TTGATGCGGTGATAACCCTTAAACCGATAATAGAAACGCAGGGAACCAGCTTTATTTTGTTGCTCCATCCTGTGGAACAGATGCGGCAGTTGATGACCAGTCAATTAGGAAAAGTCAGCCATACCTTCGCTCATATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTCATTTTGGTCGCCAGGCGGCGCGCAGTAGCTTTCCTGTCCTGCTTTGTGGAGAAGAGGGCGTGGGCAAGGCAC  >  NC_000913/1251910‑1252152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A