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
A1 F28 I1 R1 120 97.0 3206026 99.3% 3183583 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,018,976 (A)8→9 intergenic (+39/+37) matP → / ← ompA macrodomain Ter protein/outer membrane porin A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,018,9681.A95.9% 163.1 / 0.0 49intergenic (+31/+45)matP/ompAmacrodomain Ter protein/outer membrane porin A
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base A (25/22);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.62e-01

TCTGAAACGATTGTTCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGC‑‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCA  >  NC_000913/1018830‑1019100
                                                                                                                                           |                                                                                                                                     
tCTGAAACGATTGTTCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGC‑‑a                                                                                                                                     >  1:552823/1‑140 (MQ=255)
             ttCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGC‑‑AAAAAAAAaccccg                                                                                                                        <  1:102507/140‑3 (MQ=255)
               cAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCgca                                                                                                                       <  1:514417/140‑1 (MQ=255)
                  cTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCgcagca                                                                                                                    >  1:565729/1‑140 (MQ=255)
                    gATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCagcagc                                                                                                                  >  1:383589/1‑140 (MQ=255)
                     aTTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCg                                                                                                                 <  1:1189611/140‑1 (MQ=255)
                     aTTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCg                                                                                                                 >  2:1465077/1‑140 (MQ=255)
                      ttGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCgg                                                                                                                <  2:552823/140‑1 (MQ=255)
                       tGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCATTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCggg                                                                                                               <  1:1112393/140‑1 (MQ=255)
                               cGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCt                                                                                                       >  2:493694/1‑140 (MQ=255)
                               cGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCt                                                                                                       >  2:153862/1‑140 (MQ=255)
                                   aaaCAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCa                                                                                                   >  2:1058464/1‑140 (MQ=255)
                                        aaGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACga                                                                                              <  2:1554620/140‑1 (MQ=255)
                                                      aaTAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGc                                                                                <  2:759173/140‑1 (MQ=255)
                                                        tAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCgg                                                                              <  2:383589/140‑1 (MQ=255)
                                                        tAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCgg                                                                              <  1:398391/140‑1 (MQ=255)
                                                                 ttctCTGAAGCAGGATCTGTAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTAc                                                                     <  1:1009970/140‑1 (MQ=255)
                                                                 ttctCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTAc                                                                     >  2:621448/1‑140 (MQ=255)
                                                                  tctcTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACa                                                                    >  2:1266202/1‑140 (MQ=255)
                                                                  tctcTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACa                                                                    <  1:1358031/140‑1 (MQ=255)
                                                                   ctctGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACaa                                                                   >  1:372992/1‑140 (MQ=255)
                                                                    tctGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAAc                                                                  <  1:915508/140‑1 (MQ=255)
                                                                            aGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGa                                                          <  1:153862/140‑1 (MQ=255)
                                                                            aGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGa                                                          <  1:493694/140‑1 (MQ=255)
                                                                             ggATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGAt                                                         >  2:1022172/1‑140 (MQ=255)
                                                                              gATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATa                                                        >  2:901353/1‑140 (MQ=255)
                                                                              gATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATa                                                        >  2:176587/1‑140 (MQ=255)
                                                                                  tGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCtt                                                    <  1:172110/140‑1 (MQ=255)
                                                                                  tGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCtt                                                    <  1:1501497/140‑1 (MQ=255)
                                                                                   gCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCttt                                                   >  1:1333567/1‑140 (MQ=255)
                                                                                      ggCATTGCTGGGTAAGGAATAACTGAAGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAAc                                                >  1:728919/1‑140 (MQ=255)
                                                                                       gCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACt                                               >  2:7898/1‑140 (MQ=255)
                                                                                        cATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCAAAAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACt                                               >  1:1203183/1‑140 (MQ=255)
                                                                                        cATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACtt                                              <  1:206395/140‑1 (MQ=255)
                                                                                        cATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACtt                                              >  1:1195509/1‑140 (MQ=255)
                                                                                        cATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACtt                                              >  2:26980/1‑140 (MQ=255)
                                                                                                     ggAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTAcgcg                                 >  1:663143/1‑140 (MQ=255)
                                                                                                            cTGACGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATcc                          >  1:711405/1‑140 (MQ=255)
                                                                                                                cGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAg                      >  1:870893/1‑140 (MQ=255)
                                                                                                                cGAAAGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAg                      >  2:1367449/1‑140 (MQ=255)
                                                                                                                   aaGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCa                   <  1:11096/140‑1 (MQ=255)
                                                                                                                   aaGTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCa                   <  2:795508/140‑1 (MQ=255)
                                                                                                                     gTCAGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAgg                 <  1:1585768/140‑1 (MQ=255)
                                                                                                                      tCAGTTCAATTTACTAAAGGC‑‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCa               >  2:1100190/1‑140 (MQ=255)
                                                                                                                        aGTTCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAg              <  1:1501122/140‑1 (MQ=255)
                                                                                                                         gTTCAATTTACTAAAGGCAAAAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGCCGAGAACTTAAGCCTGCGGCTGGGTTACAACGTCTTTGATACCTTTAACTTCGATCTCAACGCGACGATCCGGAGCCAGGCAg              >  2:267251/1‑140 (MQ=255)
                                                                                                                           tCAATTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCg           >  1:1536147/1‑140 (MQ=255)
                                                                                                                             aaTTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGAt         <  1:176587/140‑1 (MQ=255)
                                                                                                                             aaTTTACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGAt         <  2:1333567/140‑1 (MQ=255)
                                                                                                                               tttACTAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCa       >  2:1011798/1‑140 (MQ=255)
                                                                                                                                    tAAAGGCA‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGACCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTgca  >  1:847225/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                     
TCTGAAACGATTGTTCAGCTGATTGAAGATGCGGAAAACAAAGAGAAATACGCGAATAAAATGTCTTCTCTGAAGCAGGATCTGCAGGCATTGCTGGGTAAGGAATAACTGACGAAAGTCAGTTCAATTTACTAAAGGC‑‑AAAAAAAACCCCGCAGCAGCGGGGTTTTTCTACCAGACGAGAACTTAAGCCTGCGGCTGAGTTACAACGTCTTTGATACCTTTAACTTCGATCTCTACGCGACGATCCGGAGCCAGGCAGTCGATCAGTGCA  >  NC_000913/1018830‑1019100

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A