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
A3 F50 I3 R1 283 58.3 1819865 98.8% 1798026 150.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,174,596 A→G S190S (AGT→AGC)  ycfT ← inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,174,5960AG95.8% 127.6 / NA 48S190S (AGT→AGC) ycfTinner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (21/25);  minor base C (0/2);  total (21/27)
Fisher's exact test for biased strand distribution p-value = 4.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTAAACAACCAGGCACCGACCGCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTAACGCATACAGATACCACAAGCTGG  >  NC_000913/1174452‑1174741
                                                                                                                                                 |                                                                                                                                                  
aGTAAACAACCAGGCACCGACCGCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGtt                                                                                                                                               <  2:124092/150‑1 (MQ=255)
 gTAAACAACCAGGCACCGACCGCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTc                                                                                                                                              >  2:210388/1‑150 (MQ=255)
   aaaCAACCAGGCACCGACCGCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCAtt                                                                                                                                           <  1:877043/151‑1 (MQ=255)
      caacCAGGCACCGACCGCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTccc                                                                                                                                        <  1:809003/151‑1 (MQ=255)
          cAGGCACCGACCGCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCccacc                                                                                                                                    <  2:820259/151‑1 (MQ=255)
          cAGGCACCGACCGCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCccacc                                                                                                                                    >  2:673622/1‑151 (MQ=255)
                     cgCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGa                                                                                                                         <  1:674717/151‑1 (MQ=255)
                        cAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACg                                                                                                                      >  2:520475/1‑151 (MQ=255)
                          gAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACg                                                                                                                      >  1:539917/1‑149 (MQ=255)
                           aaCGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑aaa                                                                                                                  <  2:642373/151‑1 (MQ=255)
                             cGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAAtt                                                                                                                <  2:786223/151‑1 (MQ=255)
                               gTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTa                                                                                                               >  1:527394/1‑150 (MQ=255)
                                     aaaGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGcc                                                                                                         >  1:194062/1‑150 (MQ=255)
                                             cATCAGCAGATGGCGGCGCAACGGCACCTCTTAAACACAGGTCATTATTGTTGCGCCAAACCAGGCGCCAAGG‑CTGTAAAAAGGAAAATGGCGGATCACGCTGTTCATTCCCCCCCACGGCGTGGGAACG‑AAATTAACCGCCACACTcag                                                                                                 <  2:698221/150‑1 (MQ=255)
                                                       tGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTacaaac                                                                                       >  1:752507/1‑150 (MQ=255)
                                                       tGGCGGCCCAACGCCCCCTCTTTAACACAGGTAATTATTGTTGCGCAAAACCATGCGCAAAGG‑CTGTAATAAGGAAATTTGGGGATCCCGCTGTTCTTCCCCCCCCACGGCGGGGGAACG‑AAATTAACCGCCACACTCAGCAGTacaaac                                                                                       <  2:389849/150‑1 (MQ=255)
                                                        ggcggcACAACGGCACCTCTTTAACCCAGGTCTTAATTGTTGCGCAAACCCAGGCGCCAAGG‑CTGTAAAAAGGAAAATTGCGGATCCCGCTGTTCATCCCCCCCCCCGGGGTGGGAACA‑AAATTAACCGCCACACTCAGCAGTacaaaca                                                                                      <  1:349674/150‑1 (MQ=255)
                                                         gcggcgCAACGGCCCCTCTTAAACAAAGGTCATTATTGTGGC‑CCAAACCCAGGGGCAAGGTTTAAAATAAGGAAAATTGCGGACCCCGCTTTTCATCCCCCACCACGGGGGGGAAACA‑AAATTAACCGCCACACTCAGCAGTacaaac                                                                                       <  2:42214/148‑1 (MQ=255)
                                                           ggcgCAACGGCACCTTTTTAACACAGGTCATTTTTGTTGCGCAAACCCATGCGCAAGGG‑CTGTAATAAGGAAAATTGCGGATCACGCTGTTCATCCCCCCCCACGGCGGGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGc                                                                                  <  1:389830/151‑1 (MQ=255)
                                                           ggcgAAACGGCCCCTCTATAACACAGGTCATTATTTTGGCCCCAAACCAGGCGCCAGGG‑CTGTAAAAAGGAAAATTGCGGACCCCGCTTTTCACCCCCCCCCACGGGGGGGAAACA‑AAATTAACCGCCACACTCAGCAGTACAAACAAgg                                                                                   <  2:538453/150‑1 (MQ=255)
                                                                aaCGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAAt                                                                              >  2:439226/1‑150 (MQ=255)
                                                                  cgccACCTCTTAAACAAAGTTCATTATTGTGGCGCCAACCCATGCGCCGAGG‑CTGTAAAAAGGCAAATTGCGGATCACGCTGTTCATCCCCCACCCCGGCGTGGGAACA‑AAATAAACCGCCACACTCAGCAGTACAAACAAGGCGAATa                                                                             <  2:234275/146‑1 (MQ=255)
                                                                   ggCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTg                                                                          >  1:155885/1‑151 (MQ=255)
                                                                      aCCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGc                                                                        >  1:569827/1‑150 (MQ=255)
                                                                      aCCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGc                                                                        >  2:15061/1‑150 (MQ=255)
                                                                       ccTTTTTAACACAGGTTATTTTTGTGGCGCAAAACCATGCGCCAGGG‑TTGAAATAAGGAAAATGGGGAATCACGCTGTTCATCCCCCCCCCCGGGGTGGAAAGG‑AAATAAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTgg                                                                         <  2:706978/148‑1 (MQ=255)
                                                                         tctTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAgcg                                                                    >  1:603914/1‑151 (MQ=255)
                                                                          ctTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAgcgc                                                                   >  1:483702/1‑151 (MQ=255)
                                                                           tttAACAAAGGTCATTTTTGTTGCGCAAAACCAGGCGCAAAGG‑CTGTAATAAGGAAAATTGCGGACCCCGCTGTTCATCCCCCCCCACGGCGTGGAAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAgc                                                                     <  1:170047/148‑1 (MQ=255)
                                                                           ttaaaCCCAGGTCATGATTGGGGCCCCAAACCTGCCACCAGGG‑CTGTAATAAGGAAAATTGGGGATACCGCTGTTAATCCCCCCCCCCTGCGGGGGAAAG‑AAATAAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAg                                                                      <  1:538996/144‑1 (MQ=255)
                                                                           ttaaaCACAGTTATTTATTGTGGCGCCAAACCTGGCGCCAGGG‑TTTTAAAAAGGAAAATTGCGAATCCCGCTTTTCGTCCCCCCCCCCGGGGTGGGAACA‑AAATAAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAgc                                                                     <  2:796439/145‑1 (MQ=255)
                                                                                   aGGTCATTATTGTTGCGCAAACCCATGCGCCAAGG‑CTGTAATAAGGAAAATTGCGGATCCCGCTGTTCATCCCCCCCCACGGCGGGGGAACA‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGc                                                           <  1:752326/150‑1 (MQ=255)
                                                                                      tCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTaa                                                        >  2:770840/1‑150 (MQ=255)
                                                                                        attattGTTGCGCAAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCCCCAGGGCGTGGAAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTaaaa                                                      <  1:175160/150‑1 (MQ=255)
                                                                                                        aCCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGa                                      >  2:679206/1‑150 (MQ=255)
                                                                                                        aCCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGa                                      >  1:651947/1‑150 (MQ=255)
                                                                                                           aTGCGCCAAGG‑CTGTAATAAGGCAACTTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGaaa                                    >  2:566428/1‑149 (MQ=255)
                                                                                                           aTGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAAt                                   >  1:593948/1‑150 (MQ=255)
                                                                                                                cgaggg‑CTGTAAAAAGAAAAATCGCGGACCTCCCTGTCCATACCCC‑CCACGGGGGGGGAAAGAAAATTACCCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATAc                                           <  2:79837/133‑1 (MQ=255)
                                                                                                                  aaGG‑CTGAAAAAGGGAAAATTGCGGACCACGCTGTTCATCCCCCACCACGGGGTGGAAACA‑AAATAAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACaa                             <  2:431666/149‑1 (MQ=255)
                                                                                                                    gg‑CTGAAAAAAGGAAAATTGCGGACCACGCTTTTCATCCCCCACCACGGGGTGGAAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTa                          <  2:232106/150‑1 (MQ=255)
                                                                                                                      gttGTAAAAAGGAAAATGGGGGATCACCCTTTTCATCCCCCACCCCGGCGGGGAAACA‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTAAc                        <  2:447482/149‑1 (MQ=255)
                                                                                                                              aaGGCAAATTGCGGATCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTAACGCATAc                  >  2:475044/1‑149 (MQ=255)
                                                                                                                                     aTTGCGGATCACGCTTTTCATCCCCCCCCCCGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTAACGCATACAGATACcac         <  1:280799/151‑1 (MQ=255)
                                                                                                                                      ttGCGGACCCCGCTGTTCATCCCCCACCCCGGGGTGGGAACA‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTAACGCATACAGATACcac         <  1:340576/150‑1 (MQ=255)
                                                                                                                                            aTCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTAACGCATACAGATACCACAAGCTgg  >  2:184242/1‑151 (MQ=255)
                                                                                                                                            aTCACGCTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTAACGCATACAGATACCACAAGCTgg  >  1:186101/1‑151 (MQ=255)
                                                                                                                                             tCACGCTGTTCATCCCCCTCCACGCCGTGGGAACG‑AAATAAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCTCGAAATAGACAATTAACGCATACAGATACCACAAGCTgg  <  2:362132/150‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                  
AGTAAACAACCAGGCACCGACCGCCAGAACGGTAAGCAAAGAAGCCATCAGCAGATGGCGGCGCAACGGCACCTCTTTAACACAGGTCATTATTGTTGCGCCAAACCATGCGCCAAGG‑CTGTAATAAGGCAAATTGCGGATCACACTGTTCATTCCCCACCACGGCGTGGGAACG‑AAATTAACCGCCACACTCAGCAGTACAAACAAGGCGAATAGTGGCAGCGCCAGACGGCTAAAAATTTTACATACCACGAAATAGACAATTAACGCATACAGATACCACAAGCTGG  >  NC_000913/1174452‑1174741

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A