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
A10 F54 I0 R1 1784 57.4 2855260 92.9% 2652536 134.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,610,676 G→A 100% E14K (GAA→AAA)  emrE → small multidrug resistance protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,610,6760GA100.0% 170.1 / NA 50E14K (GAA→AAA) emrEsmall multidrug resistance protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/23);  total (27/23)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAAGGTTCCACTGCTCGGCCATCAACCTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCGAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCGGTGGGGATTGCCTACGCCATC  >  NC_002947/5610529‑5610822
                                                                                                                                                   |                                                                                                                                                  
cAAGGTTCCACTGCTCGGCCATCAACCTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCaaa                                                                                                                                                  <  1:876013/150‑1 (MQ=255)
cAAGGTTCCACTGCTCGGCCATCAACCTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCaaa                                                                                                                                                  <  1:724179/150‑1 (MQ=255)
 aaGGTTCCACTGCTCGGCCATCAACCTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAg                                                                                                                                                 >  1:883489/1‑150 (MQ=255)
         aCTGCTCGGCCATCAACCTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCAAGCTCAGTAACGGAGGATCCTGACATCAATGAGTCTATTTAGTTCGCCATTGCCTGGTGGGCCAAAGTCATCGcc                                                                                                                                         >  1:1384714/1‑150 (MQ=255)
                      cAACCTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGa                                                                                                                            >  1:1034966/1‑150 (MQ=255)
                         ccTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAgg                                                                                                                         <  2:909460/150‑1 (MQ=255)
                         ccTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCATATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAgg                                                                                                                         >  2:816355/1‑150 (MQ=255)
                          cTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGc                                                                                                                        >  1:1202696/1‑150 (MQ=255)
                           tATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCg                                                                                                                       >  2:506031/1‑150 (MQ=255)
                             tctcCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGt                                                                                                                     <  1:1324703/150‑1 (MQ=255)
                             tctcCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGt                                                                                                                     <  1:506031/150‑1 (MQ=255)
                                 ccATATCGATAAGTTATGATGTTACCCAATCCAGGCAACTTCAAGAATCCCCGCTCAGTAACGGAGGATCCTACAATGAATGCCTCTACCTACCTCGCCATTGACATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGaaa                                                                                                                 <  2:605023/150‑1 (MQ=255)
                                  cATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCATATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGACAg                                                                                                                <  1:816355/150‑1 (MQ=255)
                                      tCGATCGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCTCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCt                                                                                                            <  2:1034966/150‑1 (MQ=255)
                                                 tGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCaaa                                                                                                                                                  <  2:206167/101‑1 (MQ=255)
                                                          cccATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCActgc                                                                                        >  2:1063087/1‑150 (MQ=255)
                                                           caaTCCAGGAAACGGCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCTTGAATTCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCActgct                                                                                       >  2:764650/3‑150 (MQ=255)
                                                            cATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGc                                                                                                        <  1:1264735/132‑1 (MQ=255)
                                                            cATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGc                                                                                                        >  2:1264735/1‑132 (MQ=255)
                                                             aTCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCActgctgc                                                                                     <  2:883489/150‑1 (MQ=255)
                                                                  ggCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGAtg                                                                                >  1:22040/1‑150 (MQ=255)
                                                                   gCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGAtgg                                                                               >  1:932429/1‑150 (MQ=255)
                                                                     aaCGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGAtggtg                                                                             >  2:1130400/1‑150 (MQ=255)
                                                                         tCTATAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTg                                                                         >  2:1307792/1‑150 (MQ=255)
                                                                                   ccGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGGCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCAt                                                               >  2:46011/1‑150 (MQ=255)
                                                                                           tAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCt                                                       <  2:267419/150‑1 (MQ=255)
                                                                                              cGGAGGATCCTGCCATGCGTGGCTAGGCCGACCTCGCCATTGCCATCTGCGCCAAAGTCATCGATCTTTCCGCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGa                                                    <  1:668034/150‑1 (MQ=255)
                                                                                                gaggaTCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTTCATCGAGGCGGTgg                                                                                                                   <  1:1061321/85‑2 (MQ=37)
                                                                                                gaggaTCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATg                                                  <  2:121275/150‑1 (MQ=255)
                                                                                                gaggaTCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATg                                                  >  1:121275/1‑150 (MQ=255)
                                                                                                       cTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGc                                           >  1:406129/1‑150 (MQ=255)
                                                                                                        tGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCt                                                                                                            >  2:869718/1‑84 (MQ=255)
                                                                                                        tGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCt                                                                                                            <  1:869718/84‑1 (MQ=255)
                                                                                                        tGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCt                                          >  1:115492/1‑150 (MQ=255)
                                                                                                         gCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCtg                                         <  2:22040/150‑1 (MQ=255)
                                                                                                           gaagAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCAACGCCTCGATGAAGGCGGTGAAAGGCCTGAGCAAGCCGTAACCACTGCTGCTGATGGTGTGTGGTTATGACATTGGGGGGTGGAGGCTGACGCtggg                                       >  1:760906/4‑149 (MQ=255)
                                                                                                            aTGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTAt                                                                    >  1:931162/1‑120 (MQ=255)
                                                                                                            aTGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTAt                                                                    <  2:931162/120‑1 (MQ=255)
                                                                                                                   ccTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCgca                               <  1:1063087/150‑1 (MQ=255)
                                                                                                                   ccTATACCTACCTCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCgca                               <  1:1307792/150‑1 (MQ=255)
                                                                                                                           tacctCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCg                       <  2:115492/150‑1 (MQ=255)
                                                                                                                            acctCGCCATTGCCATCTGCGCCAAAGTCATCGTCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTAt                                                                    >  1:304390/1‑104 (MQ=255)
                                                                                                                            acctCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTAt                                                                    <  2:304390/104‑1 (MQ=255)
                                                                                                                             cctCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCGGt                     <  1:1056479/150‑1 (MQ=255)
                                                                                                                              ctCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCActgctgc                                                                                     >  2:1287588/1‑85 (MQ=255)
                                                                                                                              ctCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCActgctgc                                                                                     <  1:1287588/85‑1 (MQ=255)
                                                                                                                              ctCGCCATTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCGGTg                    <  2:932429/150‑1 (MQ=255)
                                                                                                                                    aTTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCGGTGGGGAtt              >  2:320871/1‑150 (MQ=255)
                                                                                                                                    aTTGCCATCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCGGTGGGGAtt              >  2:968333/1‑150 (MQ=255)
                                                                                                                                           tCTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCGGTGGGGATTGCCTACg       >  2:1186508/1‑150 (MQ=255)
                                                                                                                                            cTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTg                                               >  2:556514/1‑109 (MQ=255)
                                                                                                                                            cTGCGCCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTg                                               <  1:556514/109‑1 (MQ=255)
                                                                                                                                                gcCAAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCGGTGGGGATTGCCTACGCCATc  >  2:309271/1‑150 (MQ=255)
                                                                                                                                                   |                                                                                                                                                  
CAAGGTTCCACTGCTCGGCCATCAACCTATCTCCCATATCGATAGGTAATGACTTTACCCCATCCAGGCAACGTCTAGAATGCCCGCTCAGTAACGGAGGATCCTGCCATGAATGCCTATACCTACCTCGCCATTGCCATCTGCGCCGAAGTCATCGCCACCGCCTCGATGAAGGCGGTGAAAGGCCTGAGCACGCCGTTGCCACTGCTGCTGATGGTGGTTGGCTATGGCATTGCGTTCTGGATGCTGACGCTGGTGGTCCGCAGCATTCCGGTGGGGATTGCCTACGCCATC  >  NC_002947/5610529‑5610822

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A