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
A4 F1 I2 R1	780	68.3	3343050	93.5%	3125751	102.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,350,162	A→G	L284L (TTG→CTG)	glpQ ←	periplasmic glycerophosphodiester phosphodiesterase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,350,162	0	A	G	96.2%	171.4 / ‑2.6	52	L284L (TTG→CTG)	glpQ	periplasmic glycerophosphodiester phosphodiesterase
Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (26/24); total (27/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01

ATTCACATCAGGAGTGTATTCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCTTCCATCCGGCTGTTTCTGCTGCGTTTCATTCCAGT  >  NC_000913/2350028‑2350293

aTTCACATCAGGAGTGTATTCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCata                                                                                                                                 >  2:1350364/1‑139 (MQ=255)

        cAGGAGTGTATTCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTaacc                                                                                                                         <  1:312177/139‑3 (MQ=255)

              tgtATTCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGACAGTGAGTTTGATATTACCCGGCTGCGATGTCTCGTCAATCAGCATATGGTAATCCGGAcc                                                                                                                   >  1:1062946/1‑139 (MQ=255)

                tATTCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACAAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCaa                                                                                                                 >  1:1180393/1‑139 (MQ=255)

                  ttCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCaa                                                                                                                 <  2:693996/137‑1 (MQ=255)

                  ttCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCaa                                                                                                                 >  1:693996/1‑137 (MQ=255)

                  ttCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATa                                                                                                               >  1:930661/1‑139 (MQ=255)

                   tCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATAc                                                                                                              <  2:930661/139‑1 (MQ=255)

                       gCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGCTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATc                                                                                                          >  1:919117/1‑139 (MQ=255)

                          gTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAAt                                                                                                                <  1:947597/130‑1 (MQ=255)

                          gTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAAt                                                                                                                >  2:947597/1‑130 (MQ=255)

                          gTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGc                                                                                                       >  1:1397515/1‑139 (MQ=255)

                          gTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGc                                                                                                       >  2:562688/1‑139 (MQ=255)

                                  gACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCg                                                                                               <  1:1323632/139‑1 (MQ=255)

                                      gCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCAc                                                                                           <  2:1397515/139‑1 (MQ=255)

                                                    tGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCAc                                                                             <  2:919117/139‑1 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGTACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGa                                                                                                                     <  2:659921/97‑1 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGTACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGa                                                                                                                     >  1:659921/1‑97 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATc                                                                                                                         >  2:1475016/1‑93 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATc                                                                                                                         <  1:1475016/93‑1 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCAccc                                                                           <  1:1666390/139‑1 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCAccc                                                                           >  2:1641338/1‑139 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCAccc                                                                           >  1:1390255/1‑139 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATc                                                                                                                         <  1:430403/93‑1 (MQ=255)

                                                      cACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATc                                                                                                                         >  2:430403/1‑93 (MQ=255)

                                                            cAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTa                                                                     <  2:1180393/139‑1 (MQ=255)

                                                                             cATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATAc                                                                                                              <  2:1606104/81‑1 (MQ=255)

                                                                             cATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATAc                                                                                                              >  1:1606104/1‑81 (MQ=255)

                                                                                  tGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAAt                                               <  1:1641338/139‑1 (MQ=255)

                                                                                       cATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAAcc                                          >  1:1291843/1‑139 (MQ=255)

                                                                                       cATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAAcc                                          <  1:562688/139‑1 (MQ=255)

                                                                                         tGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCAc                                                                                           <  2:994204/88‑1 (MQ=255)

                                                                                         tGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCa                                        >  2:381561/1‑139 (MQ=255)

                                                                                         tGCCAGTGAGTTTGATATTACCCGGCTGCGATATCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCAc                                                                                           >  1:994204/1‑88 (MQ=255)

                                                                                             aGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCtt                                    <  1:381561/139‑1 (MQ=255)

                                                                                               tGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCg                                                         <  1:911909/116‑1 (MQ=255)

                                                                                               tGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCg                                                         >  2:911909/1‑116 (MQ=255)

                                                                                                   tttGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCa                                                                                   >  1:701182/1‑86 (MQ=255)

                                                                                                   tttGATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCa                                                                                   <  2:701182/86‑1 (MQ=255)

                                                                                                      gATATTACCCGGCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCTTCCATCCGGc                           <  1:1350364/139‑1 (MQ=255)

                                                                                                                ggCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCa                                                                              >  2:499507/1‑78 (MQ=255)

                                                                                                                ggCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCa                                                                              <  1:499507/78‑1 (MQ=255)

                                                                                                                 gCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCgg                                                                         <  1:592957/82‑1 (MQ=255)

                                                                                                                 gCTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCgg                                                                         >  2:592957/1‑82 (MQ=255)

                                                                                                                  cTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGtt                                                    >  2:1382972/1‑102 (MQ=255)

                                                                                                                  cTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGtt                                                    <  1:1382972/102‑1 (MQ=255)

                                                                                                                  cTGCGATGTCTCCTCAATCAGCATATGGTAATCCGGACCAATACCATCTACATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCTTCCATCCGGCTGTTTCtgctgc               >  1:1598444/1‑139 (MQ=255)

                                                                                                                            tcctcAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAAcc                                          <  2:372310/102‑1 (MQ=255)

                                                                                                                            tcctcAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAAcc                                          >  1:372310/1‑102 (MQ=255)

                                                                                                                            tcctcAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCTTCCATCCGGCTGTTTCTGCTGCGTTTCATTcc     >  1:1209202/1‑139 (MQ=255)

                                                                                                                            tcctcAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCTTCCATCCGGCTGTTTCTGCTGCGTTTCATTcc     >  2:153277/1‑139 (MQ=255)

                                                                                                                              ctcAATCAGCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCTTCCATCCGGCTGTTTCTGCTGCGTTTCATTCCAg   <  2:1390255/139‑1 (MQ=255)

                                                                                                                               tcaatcagCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCTTCCATCCGGCTGTTTCTGCTGCGTTTCATTCCAGt  <  2:1291843/139‑1 (MQ=255)

                                                                                                                                  atcagCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCAccc                                                                           <  2:57269/63‑1 (MQ=255)

                                                                                                                                  atcagCATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCAccc                                                                           >  1:57269/1‑63 (MQ=255)

ATTCACATCAGGAGTGTATTCAGGCAGTTTATCTGACCGCACGGTATAAGGATGCACTACCAGTTTATTCTGCTGAGCATCTTGCACCATGCCAGTGAGTTTGATATTACCCGGCTGCGATGTCTCCTCAATCAACATATGGTAATCCGGACCAATACCATCTGCATATTCCGCCACCTGTTTCATGGCACCCGGCTTAAACATCCAGTCGTAGTTGTAATTAACCCAGCTTCCATCCGGCTGTTTCTGCTGCGTTTCATTCCAGT  >  NC_000913/2350028‑2350293

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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