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
A5 F1 I2 R1	77	34.8	1608548	95.0%	1528120	114.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,173,883	G→A	pseudogene (396/914 nt)	gatC ←	pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,173,883	0	G	A	100.0%	116.7 / NA	34	pseudogene (396/914 nt)	gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (18/16); total (18/16)

AATACCTTCCAGCTCAAAGAAATTTCGGGTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCGGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCGACGCCCAGGTCATTGG  >  NC_000913/2173748‑2174017

aaTACCTTCCAGCTCAAAGAAATTTCGGGTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTg                                                                                                                                     <  2:617021/139‑1 (MQ=255)

       tCCAGCTCAAAGAAATTTCGGGTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCa                                                                                                                              >  2:61280/1‑139 (MQ=255)

       tCCAGCTCAAAGAAATTTCGGGTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCa                                                                                                                              >  2:46577/1‑139 (MQ=255)

       tCCAGCTCAAAGAAATTTCGGGTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCa                                                                                                                              >  2:266298/1‑139 (MQ=255)

                       ttCGGGTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCa                                                                                                              <  1:46577/139‑1 (MQ=255)

                            gTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGatat                                                                                                         <  1:266298/139‑1 (MQ=255)

                            gTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGatat                                                                                                         <  1:363607/139‑1 (MQ=255)

                                      cAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTac                                                                                               <  2:46358/139‑1 (MQ=255)

                                            aGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCcg                                                                                         <  1:61280/139‑1 (MQ=255)

                                                   gAGCTTATACACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATa                                                                                  <  1:730565/139‑1 (MQ=255)

                                                    aGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATAc                                                                                 <  2:203895/139‑1 (MQ=255)

                                                                      gcgTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCa                                                               >  2:538601/1‑139 (MQ=255)

                                                                                ccACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATAc                                                                                 >  2:99932/1‑111 (MQ=255)

                                                                                ccACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATAc                                                                                 <  1:99932/111‑1 (MQ=255)

                                                                                        gCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCaa                                             >  2:714759/1‑139 (MQ=255)

                                                                                         ccATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGa                                                                                                                     <  1:504079/66‑1 (MQ=255)

                                                                                         ccATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGa                                                                                                                     >  2:504079/1‑66 (MQ=255)

                                                                                                tATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATc                                     >  1:783719/1‑139 (MQ=255)

                                                                                                 atcatcCATGAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCg                                    >  2:692445/1‑139 (MQ=255)

                                                                                                          gAACCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAgcg                           >  2:69413/1‑139 (MQ=255)

                                                                                                            aCCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATa                                                                                  <  2:386353/82‑1 (MQ=255)

                                                                                                            aCCGGTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATa                                                                                  >  1:386353/1‑82 (MQ=255)

                                                                                                                gTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCatat                                                                                                                           <  2:416737/37‑1 (MQ=255)

                                                                                                                gTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCatat                                                                                                                           >  1:416737/1‑37 (MQ=255)

                                                                                                                gTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATGCGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAAttt                     >  2:433934/1‑139 (MQ=255)

                                                                                                                gTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAAttt                     >  2:123399/1‑139 (MQ=255)

                                                                                                                gTTGCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAAttt                     >  2:397873/1‑139 (MQ=255)

                                                                                                                   gCCAGATGCAGCAACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCg                  <  1:660276/139‑1 (MQ=255)

                                                                                                                             gcaACGCGCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCGACGCCCAGGt        <  2:783719/139‑1 (MQ=255)

                                                                                                                                 cgcgCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCGACGCCCAGGTCAtt    >  2:789809/1‑139 (MQ=255)

                                                                                                                                 cgcgCCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCGACGCCCAGGTCAtt    <  1:205436/139‑1 (MQ=255)

                                                                                                                                   cgcCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCGACGCCCAGGt        <  1:163593/133‑1 (MQ=255)

                                                                                                                                   cgcCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCGACGCCCAGGt        >  2:163593/1‑133 (MQ=255)

                                                                                                                                   cgcCAGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCGACGCCCAGGTCATTgg  >  1:449465/1‑139 (MQ=255)

AATACCTTCCAGCTCAAAGAAATTTCGGGTATCGCGGGCAAACCAGTCGCCGAGCTTATAAACAAACGCCGCGTGAATTACCACACCTGCCATCCCTATCATCCATGAACCGGTTGCCAGATGCAGCAACGCGCCGGTGAAGGTCATATGCCAGATATTCCAGATATCAACATTTACCACCCGCGTCATACGGGTCAGTAACATCGCCACGTTAACCAGAATCGCAATCGGAATCGCCACCAGCGCAATTTGCGACGCCCAGGTCATTGG  >  NC_000913/2173748‑2174017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A