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 2,740,735 A→G L139P (CTG→CCG)  aroF ← 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,740,7350AG97.7% 144.9 / NA 43L139P (CTG→CCG) aroF3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (22/20);  minor base T (0/1);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCAGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATGGGGATC‑GTTAATT‑AACCCTTTCCAGCCGACAGTGGTACGGGGTTTTTCAAAATAGACGCG  >  NC_000913/2740593‑2740874
                                                                                                                                              |                                                                                                                                               
aaaaCCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCat                                                                                                                                         <  2:441447/150‑1 (MQ=255)
 ataccaaccGCCATGGAAAGCACGGAAGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCCCCAATTGCTGGCCAGCTAAACAGACCGCCCAGGTTTTGCGGGCTATTCGGATCTAACGGTTCCGTCACCAGTGGCGGT‑CCCat                                                                                                                                         <  2:550508/147‑1 (MQ=255)
 aaaCCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCatat                                                                                                                                       <  2:426911/151‑1 (MQ=255)
             aTGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCaa                                                                                                                           <  2:830816/151‑1 (MQ=255)
             aTGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCACATTTACCCGcc                                                                                                                              >  1:640191/1‑147 (MQ=255)
                   aGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAgcagca                                                                                                                     <  1:15069/151‑1 (MQ=255)
                   aGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAgcagca                                                                                                                     <  1:78130/151‑1 (MQ=255)
                         gAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTAc                                                                                                               <  2:4141/151‑1 (MQ=255)
                                   cACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCCTAATTACCCACCCCAGCAGCAAATTACGCGCGATc                                                                                                       >  1:13189/1‑149 (MQ=255)
                                          aGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTTACCAGCTCAAACAGCAATTTACGCGCGAGCTGCAG‑ccc                                                                                              >  2:290328/1‑150 (MQ=255)
                                                cGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTACCAGCCCAAAAAGCAAATTTCGCGCGGTCTGCCG‑CCCGGc                                                                                           >  1:846125/1‑147 (MQ=255)
                                                     ccGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTTACCAGCCCAAGCAACAATTTTCGCGCGGTCTGCAC‑CCCGGCtt                                                                                         >  2:237597/1‑144 (MQ=255)
                                                       gTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGTCCCCCTTTTAACCAACCCAA‑CCGCAATTTTCTCGCGGTCTGCGG‑CCCCGCctct                                                                                       >  2:96814/1‑144 (MQ=255)
                                                       gTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTACCAACCCAAACAACAATTTACGCGCGATCTTCAG‑CCCCGCTTCTACATc                                                                                  >  1:886360/1‑149 (MQ=255)
                                                         tGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCaaa                                                                               <  1:479008/150‑1 (MQ=255)
                                                          gTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCaaaa                                                                              <  1:654664/150‑1 (MQ=255)
                                                          gTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAag                                                                             <  2:808504/151‑1 (MQ=255)
                                                             cGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGc                                                                          <  1:394535/151‑1 (MQ=255)
                                                                   ccAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGccatcc                                                                     <  2:666519/150‑1 (MQ=255)
                                                                        tGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATg                                                                <  1:607301/150‑1 (MQ=255)
                                                                          cTGACTAGCTCAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCTGT‑CCCATATTCGCCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATgg                                                               <  1:235775/149‑1 (MQ=255)
                                                                          cTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTTCCCCGCTCCAGCAGCAACTTTCCCCCGATCTGCCG‑CCCCGCCTCTTCCTCACAAAAGCCCTCCATCTtggg                                                             >  2:179453/1‑151 (MQ=255)
                                                                            gACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATGGGGa                                                            <  1:625709/150‑1 (MQ=255)
                                                                             aCCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATGGGGAt                                                           <  2:109400/150‑1 (MQ=255)
                                                                              ccAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTCACCAGCACAAGCAGCAATTTACGCGCGGTCTGCAC‑CCCGGCCTCTACATCAAAAAAACCCTCCATATgggggt                                                           >  1:664751/1‑147 (MQ=255)
                                                                                            cGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATGGGGATC‑GTTAATT‑AACCCttt                                         <  2:698860/151‑1 (MQ=255)
                                                                                            cGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATGGGGATC‑GTTAATT‑AACCCttt                                         <  2:595382/151‑1 (MQ=255)
                                                                                             gCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑TCCATATTCAACAGCTCAAACAGCAATTTTCCCGCGGTCTCCAC‑CCCGGCGACTAACTCATAACAACCACACATAATGGGGTC‑GGTTATT‑AACCCttt                                         >  2:180807/1‑150 (MQ=255)
                                                                                              cccAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTACCAGCTCAAACAGCAATTTAAGCGCGATCTGCAG‑CCCCGCCTCTACATCAAAAAAGGCATCCCTATGGGGGTC‑GTTAATT‑AAACCctt                                         >  2:652395/1‑149 (MQ=255)
                                                                                              cccAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATGGGGATC‑GTTAATT‑AACCCttt                                         <  1:652444/149‑1 (MQ=255)
                                                                                                cAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTTCCCAGCTCAAGCAGCAATTTACGCGCGATCTTCAG‑CCCCGCTTCTACATCAAAAAAGCCATCCATATGGGGGTC‑GTTAATT‑AACCCTTTcc                                       >  1:592212/1‑149 (MQ=255)
                                                                                                  ggTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTACCCGCTCAAGCAGCAATTTACCCGCGATCTGCAG‑CCCCGCCTCTTCATCAAAAAAGCCATCCATATTGGGGGC‑GGTAATT‑AACCCTTTTCAGcc                                   >  1:389241/1‑151 (MQ=255)
                                                                                                      ttGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTACCAGCTCAAGCAGCAATTTTCGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAAAGACATCCATATTGGGGTC‑GTTAATTAAACCCTTTccgcccac                                 >  1:577035/1‑144 (MQ=255)
                                                                                                            gCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTACCCGCCCAAGCAGGAATTTAAACGCGGTCCTCCG‑CCCGGCCTTTACATCAAAAAAGCCATCCAAATGGGGATC‑GTTAATT‑AACCCTTTTCAGCCGACAGTgg                           >  1:593443/1‑149 (MQ=255)
                                                                                                             cTATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑CCCATATTTACCAACCCCAGCAGCAATTTAAGCGCGGTCTGCAA‑CCCGGCTTCTACATCAAAAAAGCCATCCATATGGGGGTC‑GGTAATT‑TAACCTTTTCAGCCGAAAGTgg                           >  1:56242/1‑148 (MQ=255)
                                                                                                              tATTCGGATCTAACGCTTCCGTCGCCAGTGGCGGT‑TCCATATTTATCAGCTCAAACAACAATTTTTGCGCGCGCTGCGG‑CCCGGCCTCTTCATCAAAAAAGCCATCCCTATGGGGGTCGGTTAATT‑AAACCTTTCC‑GCCCACAGTGGGACg                       >  2:324268/1‑151 (MQ=255)
                                                                                                                         aaCGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTCCCCGCTCAAGCAGCAATTTTAGCGCGGTCTTCAG‑ACCGGCTTCTACATCAAAAAAGCCCTCCCTATTGGGGTC‑GTTAAAT‑TAACCTTTCCAGCCCACCGTGGGACGGGGgtttt               >  1:678662/1‑148 (MQ=255)
                                                                                                                          aCGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTACCAGCTCAAACAGCAATTTTCGCGCGCGCTGCCG‑CCCCGCCTCTTAATCCAAAAAGCCCTCCCCATGGGGGGC‑GGTTATT‑AAACCCTTCCCGCCGACAGTGGGAAGGGGgttttt              >  2:672279/1‑147 (MQ=255)
                                                                                                                          aCGCTTCCGTCGCCAGTGGCGGT‑CCCCTATTTACCAACCCCAACAGCAATTTATGCGCGGTCTGCAGCCCCGGCTT‑TTCATCAAAAAAACCATCCATATGGGGGTC‑GTTTATT‑TAAACTTTTCACCCGACAGGGGGACggggggttttaa            >  2:166906/1‑142 (MQ=255)
                                                                                                                            gCTTCCGTCGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAAATTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAAAGCCATCCATATGGGGGTC‑GTTTATT‑AAACCTTTCCAGCCGACAGGGGGACGGGGGTTTTTaaaa          >  1:265887/1‑150 (MQ=255)
                                                                                                                             cTTCCGTCGCCAGTGGCGGT‑CCCCTTTTTCCCAGCCGAAACCGGCATTTATGCGCGGTCGGCCG‑CCCGGCTTTTTCATCAAAAAAGACCTCCCTTTTGGGGTT‑GTTAATT‑AACCCTTTCCAGCCGCCAGAGGGACGGGGgttttttaaa          >  2:345781/1‑144 (MQ=255)
                                                                                                                                    cGCCAGTGGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATGGGGATC‑GTTAATT‑AACCCTTTCCAGCCGACAGTGGTACGGGGTTTTTCAAAATAGAcgcg  <  1:288243/150‑1 (MQ=255)
                                                                                                                                        aGTCGCGGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCACATGGGGATC‑GTTAATT‑AACCCTTTCCAGCCGACAGTGGTACGGAGTTTTTCAAAATAGAcg    <  2:832764/144‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                               
AAAACCAACCGGCATGGAAAGCCCGGAGGCCATTTCACGGTGAGTTTGCGATTCCGTTGTACGAGCACCAATTGCTGACCAGCTAAACAGATCGCCCAGGTATTGCGGGCTATTCGGATCTAACGCTTCCGTCGCCAGTGGCAGT‑CCCATATTCACCAGCTCAAGCAGCAATTTACGCGCGATCTGCAG‑CCCGGCTTCTACATCAAAAGAGCCATCCATATGGGGATC‑GTTAATT‑AACCCTTTCCAGCCGACAGTGGTACGGGGTTTTTCAAAATAGACGCG  >  NC_000913/2740593‑2740874

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A