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
A17 F48 I1 R1	90	35.3	1199032	98.5%	1181046	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,440,769	C→A	G87G (GGG→GGT)	rpoA ←	RNA polymerase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,440,769	0	C	A	100.0%	105.1 / NA	31	G87G (GGG→GGT)	rpoA	RNA polymerase subunit alpha
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (13/18); total (13/18)

GATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCA  >  NC_000913/3440640‑3440890

gATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGt                                                                                                                 >  1:410817/1‑140 (MQ=255)

    aCGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAg                                                                                                             >  2:147393/1‑140 (MQ=255)

    aCGTGCTGCGGCTTGACGATTTCGACATCACCGTAGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTCCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAg                                                                                                             <  2:472278/140‑1 (MQ=255)

        gctgcGGCTTGCCGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAgg                                                                                                         <  1:405702/140‑1 (MQ=255)

        gctgcGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAgg                                                                                                         <  2:572132/140‑1 (MQ=255)

        gctgcGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAgg                                                                                                         <  2:508208/140‑1 (MQ=255)

           gcGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCCCCGCCAGACCTTTCAGGTTGAGCAGGAtt                                                                                                      <  1:400210/140‑1 (MQ=255)

                  gACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGa                                                                                               >  2:46425/1‑140 (MQ=255)

                            aCATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTg                                                                                     <  2:345234/140‑1 (MQ=255)

                               tCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAAc                                                                                  <  1:147393/140‑1 (MQ=255)

                                  ccGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGcc                                                                               <  2:410817/140‑1 (MQ=255)

                                        tGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCttt                                                                         >  2:143772/1‑140 (MQ=255)

                                         gggTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTATCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTg                                                                        <  2:235589/140‑1 (MQ=255)

                                          ggTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTgg                                                                       >  2:384868/1‑140 (MQ=255)

                                             gATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGc                                                                    >  2:218981/1‑140 (MQ=255)

                                                  cGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTAc                                                               <  1:527143/140‑1 (MQ=255)

                                                  cGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTAc                                                               <  1:544260/140‑1 (MQ=255)

                                                   ggCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCAGCTTTGCCCTGAACTCTCGCCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACt                                                              <  2:524418/140‑1 (MQ=255)

                                                         aGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATgta                                                        >  2:555493/1‑140 (MQ=255)

                                                         aGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATgta                                                        >  2:518164/1‑140 (MQ=255)

                                                            cacaGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATgtagta                                                     <  1:78270/140‑1 (MQ=255)

                                                              caGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTaca                                                   <  1:514797/140‑1 (MQ=255)

                                                                   ccAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATc                                              <  1:158806/140‑1 (MQ=255)

                                                                           aGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCaa                                      >  2:562306/1‑140 (MQ=255)

                                                                                  ttCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGATCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGt                               >  2:182632/1‑140 (MQ=255)

                                                                                            gAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCaa                     >  2:3485/1‑140 (MQ=255)

                                                                                                 aCTTCATCTCTGCCCTGAACCCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTGTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCgg                >  2:578650/1‑140 (MQ=255)

                                                                                                     cATCTTTGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATc            >  1:138982/1‑140 (MQ=255)

                                                                                                          ttGCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATga       <  1:143772/140‑1 (MQ=255)

                                                                                                            gCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATgaga     >  2:334037/1‑140 (MQ=255)

                                                                                                            gCCCTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATgaga     >  1:276603/1‑140 (MQ=255)

                                                                                                             cccTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGagag    <  1:384868/140‑1 (MQ=255)

                                                                                                               cTGAACTCTCACCGCCAGACCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCa  <  1:46425/140‑1 (MQ=255)

GATCACGTGCTGCGGCTTGACGATTTCGACATCACCGTCGTGGGTGATATCGGCTGCAGTCACAGGGCCAATGCCAGATTTATTCAAGGTAAGAATAACTTCATCTTTGCCCTGAACTCTCACCGCCAGCCCTTTCAGGTTGAGCAGGATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCA  >  NC_000913/3440640‑3440890

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A