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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,527,562 A→G L140P (CTG→CCG)  sgcA ← putative phosphotransferase enzyme IIA component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,527,5620AG100.0% 202.6 / NA 55L140P (CTG→CCG) sgcAputative phosphotransferase enzyme IIA component
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (29/26);  total (29/26)

AATATCCAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCAGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAAGCAG  >  NC_000913/4527436‑4527695
                                                                                                                              |                                                                                                                                     
aaTATCCAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGgc                                                                                                                                     >  1:899335/1‑129 (MQ=255)
  tatCCAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCa                                                                                                                         <  2:732134/139‑1 (MQ=255)
     ccAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCg                                                                                                                      >  1:830026/1‑139 (MQ=255)
       aGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTc                                                                                                                    <  1:273199/139‑1 (MQ=255)
         aTGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGc                                                                                                                          <  1:559729/131‑1 (MQ=255)
         aTGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGc                                                                                                                          >  2:559729/1‑131 (MQ=255)
             aGGCTCCC‑AAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTg                                                                                                             <  2:258846/139‑1 (MQ=255)
                   ccAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCAtt                                                                                                        >  2:1010744/1‑139 (MQ=255)
                          ccAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACt                                                                                                 <  1:1010744/139‑1 (MQ=255)
                             gATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGcc                                                                                              >  2:1022005/1‑139 (MQ=255)
                                tGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGtt                                                                                           <  1:20708/139‑1 (MQ=255)
                                            tCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGc                                                                               >  2:793057/1‑139 (MQ=255)
                                             cAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCg                                                                              <  2:830026/139‑1 (MQ=255)
                                                     gACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATa                                                                      >  1:1135210/1‑139 (MQ=255)
                                                                  agGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAAc                                                                                                                               >  2:720333/1‑69 (MQ=255)
                                                                  agGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAAc                                                                                                                               <  1:720333/69‑1 (MQ=255)
                                                                  agGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATgc                                                         >  1:1308411/1‑139 (MQ=255)
                                                                  agGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATgc                                                         >  1:159168/1‑139 (MQ=255)
                                                                       ttGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGa                                                    >  2:141773/1‑139 (MQ=255)
                                                                        tGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGaa                                                   <  1:141773/139‑1 (MQ=255)
                                                                        tGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGaa                                                   <  2:1135210/139‑1 (MQ=255)
                                                                            cTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGt                                               <  2:1308411/139‑1 (MQ=255)
                                                                              ggCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGt                                                                                                                     >  1:1107983/1‑67 (MQ=255)
                                                                              ggCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGt                                                                                                                     <  2:1107983/67‑1 (MQ=255)
                                                                              ggCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCa                                             >  1:619181/1‑139 (MQ=255)
                                                                               gCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCaa                                            <  2:619181/139‑1 (MQ=255)
                                                                                cGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCaaa                                           <  2:159168/139‑1 (MQ=255)
                                                                                         ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTg                                                             <  2:1257889/112‑1 (MQ=255)
                                                                                         ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTg                                                             >  1:1257889/1‑112 (MQ=255)
                                                                                         ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGa                                                    <  2:901169/121‑1 (MQ=255)
                                                                                         ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGa                                                    >  1:901169/1‑121 (MQ=255)
                                                                                         ggTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCg                                  >  1:339838/1‑139 (MQ=255)
                                                                                           tGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGaa                                                   >  1:326612/1‑120 (MQ=255)
                                                                                           tGCAGGATCATAAGCGCCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGaa                                                   <  2:326612/120‑1 (MQ=255)
                                                                                                        gcgcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGgcg                   >  2:23038/1‑139 (MQ=255)
                                                                                                          gcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCa                                                                                                          >  1:1077779/1‑50 (MQ=255)
                                                                                                          gcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCa                                                                                                          <  2:1077779/50‑1 (MQ=255)
                                                                                                          gcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGAt                                                           >  1:60236/1‑97 (MQ=255)
                                                                                                          gcCTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGAt                                                           <  2:60236/97‑1 (MQ=255)
                                                                                                           ccTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTg                >  1:1177058/1‑139 (MQ=255)
                                                                                                            cTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTTTGTGCGGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGTTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGa               >  1:879831/1‑139 (MQ=255)
                                                                                                            cTCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGa               >  1:492204/1‑139 (MQ=255)
                                                                                                             tCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCg                                                                              <  1:756470/75‑1 (MQ=255)
                                                                                                             tCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCg                                                                              >  2:756470/1‑75 (MQ=255)
                                                                                                             tCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATAtgtg                                    >  2:1144963/1‑117 (MQ=255)
                                                                                                             tCCGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATAtgtg                                    <  1:1144963/117‑1 (MQ=255)
                                                                                                              ccGTTAACCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACg             >  2:1044180/1‑139 (MQ=255)
                                                                                                                gTTAACCTGATACCGGCGCAAACAGTGCATCGTCTCTGCTGGCATTTCCCACTGCCGTTAAGCATTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCa           <  1:793057/139‑1 (MQ=255)
                                                                                                                    aCCTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAgaga       <  1:23038/139‑1 (MQ=255)
                                                                                                                      cTGATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAag     <  2:879831/139‑1 (MQ=255)
                                                                                                                        gATACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAagca   <  1:1022005/139‑1 (MQ=255)
                                                                                                                         aTACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCg                                  >  2:669708/1‑107 (MQ=255)
                                                                                                                         aTACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCg                                  <  1:669708/107‑1 (MQ=255)
                                                                                                                         aTACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAagcag  >  2:613351/1‑139 (MQ=255)
                                                                                                                         aTACCGGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAagcag  >  1:590481/1‑139 (MQ=255)
                                                                                                                              |                                                                                                                                     
AATATCCAGATGCAGGCTCCCAAAATCCAGATTGTCCAATGCCGTCAGCTCACGACCATAGTGCAGAGGATTTGCGCTGGCGAGAGAAGGGTGCAGGATCATAAGCGCCTCCGTTAACCTGATACCAGCGCAAACAGTGCATCGTCTGTGCTGGCATTTCCCACTGCCGTTAAGCGTTGTGGCGAATCAATAAACTGGCTGATGCGCTGAATGGTCAAAATATGTGCGTTGGCATCCGTGGCGCTGACGCAGAGAAGCAG  >  NC_000913/4527436‑4527695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A