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 F28 I1 R1 180 66.5 2263572 99.4% 2249990 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,344,977 T→C S87S (AGT→AGC rpoN → RNA polymerase, sigma 54 (sigma N) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,344,9770TC95.1% 196.5 / 0.4 61S87S (AGT→AGCrpoNRNA polymerase, sigma 54 (sigma N) factor
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base C (28/30);  total (29/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

GAGAGTAATCCGCTGCTTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGG  >  NC_000913/3344840‑3345094
                                                                                                                                         |                                                                                                                     
gagaGTAATCCGCTGCTTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTg                                                                                                                     >  1:1116867/1‑140 (MQ=255)
  gagTAATCCGCTGCTTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTggg                                                                                                                   <  2:623072/140‑1 (MQ=255)
    gTAATCCGCTGCTTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGac                                                                                                                 <  2:703608/140‑1 (MQ=255)
    gTAATCCGCTGCTTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGac                                                                                                                 <  2:320212/140‑1 (MQ=255)
        tCCGCTGCTTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTggg                                                                                                                   >  2:200677/1‑134 (MQ=255)
        tCCGCTGCTTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTggg                                                                                                                   <  1:200677/134‑1 (MQ=255)
           gctgctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTg                                                                                                                     >  2:309848/1‑129 (MQ=255)
           gctgctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTg                                                                                                                     <  1:309848/129‑1 (MQ=255)
            ctgctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTa                                                                                                         <  1:430689/140‑1 (MQ=255)
             tgctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTac                                                                                                        >  2:644141/1‑140 (MQ=255)
             tgctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTac                                                                                                        >  1:372044/1‑140 (MQ=255)
               ctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGac                                                                                                                 <  1:1011443/129‑1 (MQ=255)
               ctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGac                                                                                                                 >  2:1011443/1‑129 (MQ=255)
               ctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGa                                                                                                                  <  2:66108/128‑1 (MQ=255)
               ctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGa                                                                                                                  >  1:66108/1‑128 (MQ=255)
               ctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTacac                                                                                                      <  2:465628/140‑1 (MQ=255)
               ctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTacac                                                                                                      >  1:464657/1‑140 (MQ=255)
               ctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTacac                                                                                                      <  2:464657/140‑1 (MQ=255)
               ctTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTacac                                                                                                      <  2:372044/140‑1 (MQ=255)
                  gAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGc                                                                                                   >  1:1078230/1‑140 (MQ=255)
                         tCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGc                                                                                                   <  1:535115/133‑1 (MQ=255)
                         tCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGc                                                                                                   >  2:535115/1‑133 (MQ=255)
                         tCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTaca                                                                                            <  1:374497/140‑1 (MQ=255)
                         tCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTaca                                                                                            >  2:374497/1‑140 (MQ=255)
                                  aTGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGc                                                                                   >  1:74566/1‑140 (MQ=255)
                                  aTGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGc                                                                                   >  1:214233/1‑140 (MQ=255)
                                  aTGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGc                                                                                   >  2:187563/1‑140 (MQ=255)
                                    gaagaaATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCAc                                                                                 <  1:1041566/140‑1 (MQ=255)
                                         aaTCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCGTCCGGCACCAGCg                                                                            <  2:884337/140‑1 (MQ=255)
                                          aTCGACCCCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACGCCATTTACACCGCTGGTACACCATCCGGCACCAGCg                                                                            <  1:841786/139‑1 (MQ=255)
                                          aTCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCa                                                                                  >  2:1039136/1‑133 (MQ=255)
                                          aTCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCa                                                                                  <  1:1039136/133‑1 (MQ=255)
                                          aTCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCg                                                                            >  2:841786/1‑139 (MQ=255)
                                          aTCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCg                                                                            >  1:352071/1‑139 (MQ=255)
                                          aTCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCg                                                                            <  2:352071/139‑1 (MQ=255)
                                          aTCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGACGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCgg                                                                           >  2:989759/1‑140 (MQ=255)
                                              acacCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGAc                                                                       <  2:669613/140‑1 (MQ=255)
                                                          cGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTgacgac                                                           <  2:1078230/140‑1 (MQ=255)
                                                               gACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCt                                                      <  2:694689/140‑1 (MQ=255)
                                                                 cAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGc                                                    <  1:246955/140‑1 (MQ=255)
                                                                    tGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCgg                                                 >  2:496591/1‑140 (MQ=255)
                                                                         cGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTAc                                            >  2:196067/1‑140 (MQ=255)
                                                                              gACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAggg                                       >  2:691280/1‑140 (MQ=255)
                                                                                   cgccgACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGaaa                                  <  2:691067/140‑1 (MQ=255)
                                                                                   cgccgACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGaaa                                  >  2:457630/1‑140 (MQ=255)
                                                                                    gccgACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGaaa                                  <  1:423915/139‑1 (MQ=255)
                                                                                    gccgACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGaaa                                  >  2:423915/1‑139 (MQ=255)
                                                                                     ccgACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAacg                                >  2:977863/1‑140 (MQ=255)
                                                                                      cgACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCGTTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAacga                               >  2:1011680/1‑140 (MQ=255)
                                                                                          gcgcTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCa                           <  1:644141/140‑1 (MQ=255)
                                                                                            gcTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGa                         <  1:977863/140‑1 (MQ=255)
                                                                                             cTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGAc                        >  1:17834/1‑140 (MQ=255)
                                                                                             cTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGAc                        >  2:793162/1‑140 (MQ=255)
                                                                                                   cAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCa                  <  1:989759/140‑1 (MQ=255)
                                                                                                     aaaaGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAgg                <  2:1116867/140‑1 (MQ=255)
                                                                                                     aaaaGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAgg                <  1:457630/140‑1 (MQ=255)
                                                                                                      aaaGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGa               >  2:779843/1‑140 (MQ=255)
                                                                                                           gaTGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTAcc          <  1:793162/140‑1 (MQ=255)
                                                                                                            aTGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCt         >  1:357324/1‑140 (MQ=255)
                                                                                                            aTGCCGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCt         <  1:1036187/140‑1 (MQ=255)
                                                                                                                cGGAAGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGAtg     >  2:24524/1‑140 (MQ=255)
                                                                                                                   aaGAGCTGCCGCTCGATGCCAGCTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTgg  <  2:17834/140‑1 (MQ=255)
                                                                                                                                         |                                                                                                                     
GAGAGTAATCCGCTGCTTGAGCAAATCGACACTCATGAAGAAATCGACACCCGCGAAACGCAAGACAGTGAAACGCTGGACACCGCCGACGCGCTCGAACAAAAAGAGATGCCGGAAGAGCTGCCGCTCGATGCCAGTTGGGACACCATTTACACCGCTGGTACACCATCCGGCACCAGCGGTGACTACATTGACGACGAGCTGCCGGTCTACCAGGGCGAAACGACGCAGACCTTGCAGGATTACCTGATGTGG  >  NC_000913/3344840‑3345094

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