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
A25 F111 I0 R1	33	34.4	1317450	90.1%	1187022	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	754,446	A→G	100%	L8P (CTC→CCC)	gltA ←	citrate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	754,446	0	A	G	100.0%	93.7 / NA	32	L8P (CTC→CCC)	gltA	citrate synthase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (20/12); total (20/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTCGCAGGATGCGGTTGAAGTGAAGCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGG  >  NC_000913/754307‑754581

ttCGCAGGATGCGGTTGAAGTGAAGCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGCGGGTGGGtt                                                                                                                                      >  1:381122/1‑143 (MQ=255)

               tgaagtgaagCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCGTTTTAGGACGTCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAg                                                                                                                       >  2:393885/1‑143 (MQ=255)

                  agtgaagCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCGGTGTCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCa                                                                                                                    >  2:550575/1‑143 (MQ=255)

                                     gTGAACACACCTTTTGAACCGAGCGTACGGCTATCACTAACATCTTTACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAgcgc                                                                                                 <  2:579933/143‑1 (MQ=255)

                                     gTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAgcgc                                                                                                 <  1:489903/143‑1 (MQ=255)

                                           acacCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTAtt                                                                                           >  1:420266/1‑143 (MQ=255)

                                             acCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGc                                                                                         >  1:12068/1‑143 (MQ=255)

                                                ttttGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTATCAGCACCTCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGGCTCCTTTGCGCCGTAttatgta                                                                                      >  2:500603/1‑138 (MQ=255)

                                                 tttGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGtga                                                                                     >  1:46800/1‑141 (MQ=255)

                                                    gAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCGCCGTTGAGGGTGGGTTTTGCTTTTGTATTAGCCATTTAAGGTCTTGTTAGCGTCTTATTGCGTAAGAc                                                                                  >  1:287975/1‑143 (MQ=255)

                                                     aaCCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATCTAAGGTCTCCTTAGCGCCTAATTGCGTAAGACt                                                                                 >  2:331534/1‑143 (MQ=255)

                                                       ccGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGc                                                                               >  1:285090/1‑143 (MQ=255)

                                                            agTACGGATATCCCTAACATCCTGACCGCGCGTGCCTTTCAGCACATCCAGTTCTACAGCTGTATCCCCGTTTAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGaa                                                                          <  2:244052/143‑1 (MQ=255)

                                                            agTACGGATATCACTAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGaa                                                                          <  2:335044/143‑1 (MQ=255)

                                                               aCGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACAGCCGGAACtt                                                                       >  2:571540/1‑143 (MQ=255)

                                                                          tAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGCGGGTTTTGCTTTTGTATCAGCCACTTAAGGTCGCCTTAGCGCCTTGTTGCGTCAGACTGCCGGAACTTAAATTTGCGtt                                                            >  2:567913/1‑143 (MQ=255)

                                                                                 ttGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACAt                                                     >  1:437454/1‑143 (MQ=255)

                                                                                             gCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCttt                                         <  1:231144/143‑1 (MQ=255)

                                                                                                     gCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAATACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGttt                                 >  1:550022/1‑143 (MQ=255)

                                                                                                     gCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGttt                                 <  1:607029/143‑1 (MQ=255)

                                                                                                         aTCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTa                             >  2:385900/1‑143 (MQ=255)

                                                                                                           ccAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGACTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACCTCAACCTGTCGTTGACCGCTTTTTAtg                           >  2:61631/1‑142 (MQ=255)

                                                                                                            cAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTAttt                          <  1:559412/143‑1 (MQ=255)

                                                                                                            cAGTTCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTAtttttttt                          >  2:556569/1‑143 (MQ=255)

                                                                                                               ttCAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGACCTTGAATTTGCCTTCGCACATCAACCTGGCTTTACCCGGTTTTTATTTGGc                       >  1:37768/1‑143 (MQ=255)

                                                                                                                 cAACAGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTc                     <  2:420266/143‑1 (MQ=255)

                                                                                                                     aGCTGTATCCCCGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTcgccg                 >  2:272188/1‑143 (MQ=255)

                                                                                                                         gTATCCCCGTTGAGGGGGGGTTTTGCTTTTGTATCAGCCATTTAGGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGctct             <  2:154379/143‑1 (MQ=255)

                                                                                                                             ccccGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCAATTAAGGTCTCCTTAGCGCCTAATTGCGTAAGACTGCCGGAACTTAAATTTGCCTGCGCACCTCAACCTGGCTTTACCCGTATTCTATTTGGGTCGCCGCGCGGTGa         >  1:360195/1‑143 (MQ=255)

                                                                                                                               ccGTTGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCTGTGaaa       <  1:38861/143‑1 (MQ=255)

                                                                                                                                   tGAGGGTGGGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAgg   <  2:578695/143‑1 (MQ=255)

                                                                                                                                    gAGGGTGGGTTTTGCTTTTGTACCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGAATGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAggg  <  1:331534/143‑1 (MQ=255)

TTCGCAGGATGCGGTTGAAGTGAAGCCTGGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTTTCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGGTCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGG  >  NC_000913/754307‑754581

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