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
A11 F142 I1 R1 99 64.8 3148104 96.3% 3031624 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,324,454 G→T Q238K (CAA→AAA)  phnC ← phosphonate ABC transporter ATPase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,324,4540GT95.1% 205.8 / 3.2 61Q238K (CAA→AAA) phnCphosphonate ABC transporter ATPase
Reads supporting (aligned to +/- strand):  ref base G (2/1);  new base T (32/26);  total (34/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.14e-01

TCCTCAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTGGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGCAGCGTGACGACCAC  >  NC_000913/4324359‑4324550
                                                                                               |                                                                                                
tCCTCAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTgctg                                                                                              >  1:1040548/1‑100 (MQ=255)
 ccTCAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTGgctgc                                                                                             >  1:868161/1‑100 (MQ=255)
  cTCAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAACACGTTCGTTATCAAGCTGTTTgctgct                                                                                            >  2:1299942/1‑100 (MQ=255)
  cTCAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTgctgct                                                                                            >  1:1225709/1‑100 (MQ=255)
  cTCAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTgctgct                                                                                            >  2:104040/1‑100 (MQ=255)
    cAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTtgctgctgc                                                                                          >  2:847768/1‑100 (MQ=255)
    cAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTtgctgctgc                                                                                          >  2:847753/1‑100 (MQ=255)
    cAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTtgctgctgc                                                                                          <  1:858791/100‑1 (MQ=255)
       tgatgGTGATGTCAGGCAGATTTCGCGTTCTCTTCTACGCGGGTGATGCTGCGGTAGAGATGGGCAAAACGTTTGTTATCAATCTGTTTgctgctn                                                                                           <  2:677842/96‑2 (MQ=255)
         atgGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGTCGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCcgtcg                                                                                     <  2:1397126/100‑1 (MQ=255)
          tgGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCcgtcgt                                                                                    <  1:847774/100‑1 (MQ=255)
          tgGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCcgtcgt                                                                                    <  1:847759/100‑1 (MQ=255)
          tgGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCcgtcgt                                                                                    <  2:1429768/100‑1 (MQ=255)
           ggggATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTa                                                                                   >  2:902141/1‑100 (MQ=255)
           ggggATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTa                                                                                   >  1:1552129/1‑100 (MQ=255)
            gggATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTag                                                                                  <  2:27095/100‑1 (MQ=255)
            gggATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTag                                                                                  >  2:509435/1‑100 (MQ=255)
             ggATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTaga                                                                                 <  2:362775/100‑1 (MQ=255)
                    aGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTg                                                                          >  1:198459/1‑100 (MQ=255)
                    aGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTg                                                                          >  1:366424/1‑100 (MQ=255)
                     ggCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGc                                                                         >  1:1323273/1‑100 (MQ=255)
                            ttCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGgc                                                                  <  1:1522286/100‑1 (MQ=255)
                            ttCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGgc                                                                  >  1:1377131/1‑100 (MQ=255)
                               gcgTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCa                                                               >  1:47107/1‑100 (MQ=255)
                               gcgTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCa                                                               <  1:1403750/100‑1 (MQ=255)
                               gcgTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCa                                                               >  1:69723/1‑100 (MQ=255)
                                  tgctctTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAGGACGTGCCCCTGGCGCAggg                                                            <  2:956959/98‑1 (MQ=255)
                                    ctctTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGcg                                                          <  2:398986/100‑1 (MQ=255)
                                    ctctTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGcg                                                          <  1:1560543/100‑1 (MQ=255)
                                    ctctTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTGGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGcg                                                          >  1:864386/1‑100 (MQ=255)
                                      ctTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGcgac                                                        >  1:735558/1‑100 (MQ=255)
                                       ttCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGcgacg                                                       <  2:431551/100‑1 (MQ=255)
                                         cGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGAt                                                     >  2:1243497/1‑100 (MQ=255)
                                         cGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGAt                                                     >  2:367898/1‑100 (MQ=255)
                                            cgcgGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCg                                                  >  2:1407320/1‑100 (MQ=255)
                                            cgcgGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCg                                                  <  2:430989/100‑1 (MQ=255)
                                              cgGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGtt                                                >  1:1254959/1‑100 (MQ=255)
                                              cgGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGtt                                                <  2:739053/100‑1 (MQ=255)
                                              cgGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGtt                                                <  1:1510255/100‑1 (MQ=255)
                                                 ttAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGc                                             <  1:382558/100‑1 (MQ=255)
                                                   aaTGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTGGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAg                                           <  2:864379/100‑1 (MQ=255)
                                                    aTGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGt                                          >  2:580870/1‑100 (MQ=255)
                                                     tgctgcGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTa                                         <  1:1243505/100‑1 (MQ=255)
                                                      gctgcGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAg                                        >  2:1507052/1‑100 (MQ=255)
                                                        tgcGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAgcg                                      <  1:620613/100‑1 (MQ=255)
                                                            gTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAgg                                  >  1:1001068/1‑100 (MQ=255)
                                                            gTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAgg                                  >  1:999987/1‑100 (MQ=255)
                                                                 gaTGGTCAAAACGTTCGTTATCAGACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTa                             >  2:238021/1‑100 (MQ=255)
                                                                   tGGTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAAt                           >  2:298086/1‑100 (MQ=255)
                                                                     gTCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATcc                         <  1:1560741/100‑1 (MQ=255)
                                                                      tCAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCa                        >  2:914766/1‑100 (MQ=255)
                                                                       cAAAACGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCAc                       >  2:555496/1‑100 (MQ=255)
                                                                         aaaCGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCt                     >  2:429459/1‑100 (MQ=255)
                                                                         aaaCGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCt                     <  1:154637/100‑1 (MQ=255)
                                                                          aaCGTTCGTTATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTg                    >  1:603291/1‑100 (MQ=255)
                                                                             gttcgttATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATg                 >  2:380798/1‑100 (MQ=255)
                                                                              ttcgttATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGc                <  2:69723/100‑1 (MQ=255)
                                                                               tcgttATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAAGCCACCTGATGCa               <  1:1032670/100‑1 (MQ=255)
                                                                                cgttATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGCAg              <  1:642970/100‑1 (MQ=255)
                                                                                cgttATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGCAg              <  1:643010/100‑1 (MQ=255)
                                                                                   tATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGCAGCGt           >  2:1176301/1‑100 (MQ=255)
                                                                                   tATCAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGCAGCGt           <  2:429918/100‑1 (MQ=255)
                                                                                      cAAACTGTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGCAGCGTgac        >  2:734268/1‑100 (MQ=255)
                                                                                            gTTTGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGCAGCGTGACGACCAc  >  2:1021746/1‑100 (MQ=255)
                                                                                               |                                                                                                
TCCTCAATGATGGGGATGTCAGGCAGCTTTCGCGTTCTCTTCGACGCGGTTAATGCTGCGGTAGAGATGGTCAAAACGTTCGTTATCAAACTGTTGGCTGCTGCCGTCGTAGAAGACGTGCCCCTGGCGCAGGGCGACGATGCGTTCGCAGTAGCGCAGGGCGTAATCCACCTGATGCAGCGTGACGACCAC  >  NC_000913/4324359‑4324550

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A