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
A7 F68 I0 R1 360 76.3 2813080 96.4% 2711809 135.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 3,986,382 C→T 48.1% L624F (CTC→TTC)  cyaA → adenylate cyclase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092733,986,3820CT48.1% ‑0.1 / 80.7 52L624F (CTC→TTC) cyaAadenylate cyclase
Reads supporting (aligned to +/- strand):  ref base C (14/13);  new base T (7/18);  total (21/31)
Fisher's exact test for biased strand distribution p-value = 9.71e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.50e-01

TGTCTTCAGCTTTGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTTCTGAGTGTATTGAATTGCGTCTTTC  >  CP009273/3986249‑3986512
                                                                                                                                     |                                                                                                                                  
tGTCTTCAGCTTTGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCa                                                                                                                              <  2:589148/140‑1 (MQ=255)
tGTCTTCAGCTTTGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCa                                                                                                                              <  2:406682/140‑1 (MQ=255)
tGTCTTCAGCTTTGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCa                                                                                                                              <  2:704316/140‑1 (MQ=255)
   cTTCAGCTTTGGCGAGAATCAAAAGTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCaaaa                                                                                                                           <  2:1087382/140‑1 (MQ=255)
   cTTCAGCTTTGGCGAGAATCAAAAGTGCCTGGTAGGTAGCGTTGACCGGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCaaaa                                                                                                                           <  2:1087389/140‑1 (MQ=255)
        gCTTTGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCAt                                                                                                                      >  2:90685/1‑140 (MQ=255)
        gCTTTGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCAt                                                                                                                      >  2:871780/1‑140 (MQ=255)
            tGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAgg                                                                                                                  >  2:478364/1‑140 (MQ=255)
              gCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGAc                                                                                                                >  1:228298/1‑140 (MQ=255)
                  gaATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGAcgccg                                                                                                            <  1:1397358/140‑1 (MQ=255)
                  gaATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGAcgccg                                                                                                            <  2:437327/140‑1 (MQ=255)
                  gaATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGAcgccg                                                                                                            <  2:350097/140‑1 (MQ=255)
                  gaATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGAcgccg                                                                                                            <  2:236774/140‑1 (MQ=255)
                   aaTCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGAcgccgc                                                                                                           >  2:551658/1‑140 (MQ=255)
                   aaTCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGAcgccgc                                                                                                           >  2:549949/1‑140 (MQ=255)
                   aaTCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGAcgccgc                                                                                                           >  1:1089072/1‑140 (MQ=255)
                    aTCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCa                                                                                                          <  1:1012663/140‑1 (MQ=255)
                    aTCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCa                                                                                                          <  1:1303726/140‑1 (MQ=255)
                            tGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATTATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGa                                                                                                  <  2:1022373/140‑1 (MQ=255)
                            tGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTAGGCAAAATGAATCAGTACGCCGCACCGCCAGa                                                                                                  <  2:62212/140‑1 (MQ=255)
                              ccTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATa                                                                                                <  2:90426/140‑1 (MQ=255)
                              ccTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATa                                                                                                <  2:91105/140‑1 (MQ=255)
                              ccTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATa                                                                                                >  2:301168/1‑140 (MQ=255)
                              ccTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATa                                                                                                <  2:995320/140‑1 (MQ=255)
                              ccTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATa                                                                                                <  2:236046/140‑1 (MQ=255)
                              ccTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATa                                                                                                <  2:140844/140‑1 (MQ=255)
                              ccTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATa                                                                                                <  2:1033328/140‑1 (MQ=255)
                                      gtagCGTTGACCTGCTGTACCGCAACTCGTGGAACGCAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGCTCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGaa                                                                                        <  2:33627/140‑1 (MQ=255)
                                        agCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGt                                                                                      >  1:644084/1‑140 (MQ=255)
                                                    ctgTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAg                                                                          >  1:1054882/1‑140 (MQ=255)
                                                    ctgTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAg                                                                          >  1:198661/1‑140 (MQ=255)
                                                            cAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATc                                                                  >  2:359514/1‑140 (MQ=255)
                                                               cTCGTGGAACGAAGTGCGTACGCTGCACGTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTgc                                                               <  1:822717/140‑1 (MQ=255)
                                                                tCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTgcg                                                              <  2:623350/140‑1 (MQ=255)
                                                                tCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTgcg                                                              <  1:478364/140‑1 (MQ=255)
                                                                         gAAGTGCGTACGCTGCACTTCAACGGCGAGAAATCGATGATCGATGCCCTGCTAACTATGCTCTGCACCATGCATCAGGACGCCGCAACTGCAGATAGCGTGGAAGTGTTCAGTTATAGCCAGCATCTGCGCGGCTTAAt                                                     >  2:310071/1‑140 (MQ=255)
                                                                                     cTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGt                                         <  1:1323250/140‑1 (MQ=255)
                                                                                     cTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGt                                         <  1:1328092/140‑1 (MQ=255)
                                                                                       gCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTgc                                       >  2:743915/1‑140 (MQ=255)
                                                                                       gCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTgc                                       >  2:741201/1‑140 (MQ=255)
                                                                                       gCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTgc                                       >  2:1358050/1‑140 (MQ=255)
                                                                                         aCTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTgcag                                     >  2:386045/1‑140 (MQ=255)
                                                                                             cAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAAc                                 <  1:314692/140‑1 (MQ=255)
                                                                                             cAACGGAGAGCAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACGCGCGTGCAGCAAc                                 <  1:277336/140‑1 (MQ=255)
                                                                                              aaCGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACt                                >  2:79209/1‑140 (MQ=255)
                                                                                              aaCGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACt                                >  2:1137047/1‑140 (MQ=255)
                                                                                                     aGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTTCt                         <  1:650278/140‑1 (MQ=255)
                                                                                                     aGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTTCt                         <  1:1133710/140‑1 (MQ=255)
                                                                                                       cAATCGATGATCGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTTCTGa                       <  2:542981/140‑1 (MQ=255)
                                                                                                                  cGAAGCCCTGAAAACTATTTTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTTCTGAGTGTATTGAAt            <  2:228298/140‑1 (MQ=255)
                                                                                                                            aaaaCTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTTCTGAGTGTATTGAATTGCGTCTTTc  >  1:1230114/1‑140 (MQ=255)
                                                                                                                            aaaaCTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCAAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTGATGAGTGTATTGAATTGCGTCTTTc  >  1:457838/1‑140 (MQ=255)
                                                                                                                                     |                                                                                                                                  
TGTCTTCAGCTTTGGCGAGAATCAAAATTGCCTGGTAGGTAGCGTTGACCTGCTGTACCGCAACTCGTGGAACGAAGTGCGTACGCTGCACTTCAACGGCGAGCAATCGATGATCGAAGCCCTGAAAACTATTCTCGGCAAAATGCATCAGGACGCCGCACCGCCAGATAGCGTGGAAGTCTTCTGTTATAGCCAGCATCTGCGCGGCTTAATTCGTACTCGCGTGCAGCAACTGGTTTCTGAGTGTATTGAATTGCGTCTTTC  >  CP009273/3986249‑3986512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A