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 F1 I2 R1 777 59.2 2955938 92.5% 2734242 106.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 472,742 (G)6→7 coding (145/339 nt) glnK → nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913472,7361.G97.6% 137.1 / ‑3.4 41coding (139/339 nt)glnKnitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (21/19);  total (22/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

ATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACG  >  NC_000913/472598‑472862
                                                                                                                                           |                                                                                                                               
aTGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTAcc                                                                                                                                  >  1:1243042/1‑139 (MQ=255)
     gCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑ggg                                                                                                                           >  1:68105/1‑139 (MQ=255)
        ggTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gggggc                                                                                                                        >  2:1171983/1‑137 (MQ=255)
         gTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gggggcg                                                                                                                       >  1:1256914/1‑136 (MQ=255)
         gTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gggggcg                                                                                                                       >  1:588957/1‑136 (MQ=255)
         gTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gggggcg                                                                                                                       >  1:532265/1‑136 (MQ=255)
         gTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gg                                                                                                                            >  1:1258874/1‑134 (MQ=255)
         gTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gg                                                                                                                            <  2:1258874/134‑1 (MQ=255)
              cGTGATAATCAAACCATTCAAGCTGGAGGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATa                                                                                                                   >  1:1050609/1‑139 (MQ=255)
              cGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATa                                                                                                                   >  1:760076/1‑139 (MQ=255)
                              ttCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCGATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCCTCAGAAAGGGCATGACGAGCTGTACC‑GGCGGGCCGGAATACAGCGGCAGTTTACTg                                                                                                   >  1:1375761/1‑139 (MQ=255)
                                 aaGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCa                                                                                                <  2:566526/139‑1 (MQ=255)
                                   gCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCaaa                                                                                              <  1:1171983/139‑1 (MQ=255)
                                            cGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAAt                                                                                     <  2:760076/139‑1 (MQ=255)
                                             gTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑ggggg                                                                                                                         >  1:432073/1‑100 (MQ=255)
                                             gTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑ggggg                                                                                                                         <  2:432073/101‑2 (MQ=255)
                                                       cGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGa                                                                          <  2:532265/139‑1 (MQ=255)
                                                             cTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCtg                                                                    <  2:1184051/139‑1 (MQ=255)
                                                                    tGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gg                                                                                                                            >  2:32699/1‑75 (MQ=255)
                                                                    tGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gg                                                                                                                            <  1:32699/75‑1 (MQ=255)
                                                                      gTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCa                                                             >  2:431248/1‑137 (MQ=255)
                                                                      gTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCa                                                             <  1:431248/137‑1 (MQ=255)
                                                                      gTATTCAGGGCCTGACCGACACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAAc                                                           >  1:816999/1‑139 (MQ=255)
                                                                             gggCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGa                                                    >  2:1300871/1‑139 (MQ=255)
                                                                              ggCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCaa                                                                                               <  1:239271/95‑1 (MQ=255)
                                                                              ggCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCaa                                                                                               >  2:239271/1‑95 (MQ=255)
                                                                              ggCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGaa                                                   >  1:645310/1‑139 (MQ=255)
                                                                              ggCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGaa                                                   >  2:7259/1‑139 (MQ=255)
                                                                               gCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAg                                                  >  1:395229/1‑139 (MQ=255)
                                                                                 cTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTg                                                >  1:98776/1‑139 (MQ=255)
                                                                                  tGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGa                                               >  2:628865/1‑139 (MQ=255)
                                                                                   gACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGAt                                              >  1:493705/1‑139 (MQ=255)
                                                                                   gACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGAt                                              >  1:747650/1‑139 (MQ=255)
                                                                                       gTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAGGTGATCGat                                          <  2:1256914/139‑1 (MQ=255)
                                                                                       gTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGat                                          <  2:98776/139‑1 (MQ=255)
                                                                                       gTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGat                                          <  2:1050609/139‑1 (MQ=255)
                                                                                       gTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGat                                          <  2:588957/139‑1 (MQ=255)
                                                                                         cACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGatat                                        <  2:68105/139‑1 (MQ=255)
                                                                                          aCCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGAtgt                                                                               >  2:315973/1‑99 (MQ=255)
                                                                                          aCCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGAtgt                                                                               <  1:315973/99‑1 (MQ=255)
                                                                                          aCCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGa                                                                          <  2:67164/104‑1 (MQ=255)
                                                                                          aCCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGa                                                                          >  1:67164/1‑104 (MQ=255)
                                                                                                 tGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAATGATCGATATCGTCAGTa                                <  2:645310/139‑1 (MQ=255)
                                                                                                   aaaGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAg                              <  2:816999/139‑1 (MQ=255)
                                                                                                   aaaGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAg                              <  1:1300871/139‑1 (MQ=255)
                                                                                                   aaaGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gg                                                                                                                            >  1:168226/1‑44 (MQ=255)
                                                                                                   aaaGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑gg‑gg                                                                                                                            <  2:168226/44‑1 (MQ=255)
                                                                                                    aaGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAgg                             <  2:395229/139‑1 (MQ=255)
                                                                                                     aGGTTTCGGGCGTCAGAAAGGGCATGCAGAGCAGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAggc                            >  1:874982/1‑139 (MQ=255)
                                                                                                           cGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCCGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTa                      >  2:145439/1‑139 (MQ=255)
                                                                                                                 tCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCa                                                                                                           >  2:768618/1‑48 (MQ=255)
                                                                                                                 tCAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCa                                                                                                           <  1:768618/48‑1 (MQ=255)
                                                                                                                  cAGAAAGGGCATGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGAAGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGa               >  1:1338553/1‑139 (MQ=255)
                                                                                                                            aTGCCGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCg     >  1:948677/1‑139 (MQ=255)
                                                                                                                               ccGAGCTGTACCGGG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACg  >  2:344601/1‑139 (MQ=255)
                                                                                                                                           |                                                                                                                               
ATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACC‑GG‑GGGGCGGAATACAGCGTCAATTTCCTGCCAAAAGTAAAAATTGATGTGGCGATTGCTGATGACCAACTCGATGAAGTGATCGATATCGTCAGTAAGGCGGCTTACACCGGAAAAATTGGCGACG  >  NC_000913/472598‑472862

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A