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
A14 F56 I20 R2 1958 92.1 3575798 91.1% 3257551 126.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 2,197,928 T→C S70S (TCA→TCG)  U712_11010 ← Chorismate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068812,197,9280TC98.0% 154.5 / ‑4.7 52S70S (TCA→TCG) U712_11010Chorismate synthase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (15/35);  total (16/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-01

AAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATTTGGCGCTTCATTTCCTTTTCTTCATCCTCTGTAATCGGAGCCGCACCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACGACGAGAGCAATTGGTGAACCGAGTGTTCGTGCATGACGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GGCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTA  >  CP006881/2197794‑2198062
                                                                                                                                      |                                                                                                                                       
aaGTCAGCGTGCCCAGGTCGCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGTGaa                                                                                                                                      <  6:249005/138‑1 (MQ=255)
aaGGCAGCGGGCCCAGGTCTCGGGCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGaa                                                                                                                                      <  6:75066/138‑1 (MQ=255)
 aggcAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                                                                                    <  6:444032/136‑1 (MQ=255)
 aGTGAGCGTGCCCAGGTCTCGGTCAGGAAATCTGGCGCTTCTTTTCCTTTTCTTCCTCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                                                                                    <  4:360783/139‑1 (MQ=255)
 aGTCTGCGTGCCCAGGGCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTGCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCTATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                                                                                    <  8:52533/139‑1 (MQ=255)
 aGTCAGCGTGCCCAGGTCTCGGGCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                                                                                    <  7:269881/139‑1 (MQ=255)
  gTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCGTCATTTCCTTTTCTTCATCTTATGTTATCGGAGCGGCGCCCAAGATTTTTGTCCAATGCTTCGAATAGTTATTTTAAACTACGAGGGCAATTGGAGAACCg                                                                                                                                   >  8:239831/1‑139 (MQ=255)
   gacaggTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGa                                                                                                                                  <  3:274562/134‑1 (MQ=255)
       cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTGATTTCCTTTTCTTCGTCTTCTGTAATCGGTGCGGCGGCCATGTTTTTTGTGCAATGGTTCCAAACGTTATTTTCAAATAGGAGAGCAATTGGCGAGCCGGgtgt                                                                                                                              >  3:26423/1‑139 (MQ=255)
       cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTGATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCCTGATTTTTTTCCACTGCTTCCAATCGTTTTTTTGAACTACGAGAGCAATTGGCGCACCGAgtg                                                                                                                               >  3:43522/1‑138 (MQ=255)
       cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTGTTCATCTTCTGTTATCGGAGCGGCGCCCCTGTTTTTTGTCCAATGCTTCCAATCGTTATTTTGAACTACGAGAGCAATTGGCGGACCGAggg                                                                                                                               >  3:278188/1‑136 (MQ=255)
       cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTGATCTTCTGTAATCGGAGCGGCGCCCATGGTTTTTGTGCAATGCTTCCAATCGTTTTTTTGAACAAAGAGAGCAATTGGCGAAACGAgtg                                                                                                                               >  1:82333/1‑138 (MQ=255)
       cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAgtgt                                                                                                                              <  7:15602/139‑1 (MQ=255)
       cGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATATTCTTTAATCCGAGCGGCGCCCCATATTTTTGTGCAAAGATTCCAATCGTTAATTTAAACAACGACACCAAATGGCGAAACGAgtg                                                                                                                               >  5:71953/1‑138 (MQ=255)
       cGTGCCCAGGTCTCGGGCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTACTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAgtgt                                                                                                                              <  3:134128/139‑1 (MQ=255)
       cGTGCCCAGGGCTCGGGCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGACCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAgtgt                                                                                                                              <  7:22065/139‑1 (MQ=255)
        gTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCAATTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAgtgta                                                                                                                             <  2:182076/139‑2 (MQ=255)
              aGGTCTCGGTCTGGAAATCTTGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCa                                                                                                                       <  5:186526/139‑1 (MQ=255)
                     ggTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAAATACGATAGCAATTTGCGAACCGAGTGTACGTTCCTGGCGCa                                                                                                                >  7:423394/1‑139 (MQ=255)
                     ggTCTGGAAATCTGGCGCTTCAGTTCCTTTTAGTGATCTTCTGTAATCGGAGAGGCGCCCATGATTTTTGTCAAATGCGTACAATCGTTATTTTCAACTACGATCGGAATTGGCGCCCCGAGTGTACGTGCCTGGCGCa                                                                                                                >  6:174228/1‑139 (MQ=255)
                       tCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCAcc                                                                                                              <  3:68683/139‑1 (MQ=255)
                          ggAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                                                                                    >  4:270059/1‑114 (MQ=255)
                          ggAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAAcc                                                                                                                                    <  3:270059/114‑1 (MQ=255)
                             aaTCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTc                                                                                                        <  4:341121/139‑1 (MQ=255)
                              atctGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCa                                                                                                       <  5:398283/136‑1 (MQ=255)
                              atctGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCa                                                                                                       <  3:144643/136‑1 (MQ=255)
                                 tGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATaa                                                                                                    >  5:419096/1‑139 (MQ=255)
                                   gcgcTTCATTTGCTTTTGTTGATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTGCCATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTTGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAAtt                                                                                                  >  8:301247/1‑139 (MQ=255)
                                   gcgcTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAAtt                                                                                                  <  6:259902/139‑1 (MQ=255)
                                          aTTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGcc                                                                                            <  6:223694/138‑1 (MQ=255)
                                                        aTCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGAt                                                                              <  1:177708/138‑1 (MQ=255)
                                                          cttctGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTg                                                                           >  3:284585/3‑139 (MQ=255)
                                                              tGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGGCTGGTCGTTTTCGATCTGCATg                                                                       >  2:127216/1‑139 (MQ=255)
                                                                tAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATgcg                                                                     <  1:23008/139‑1 (MQ=255)
                                                                       aGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGgcggccg                                                              >  3:400046/1‑139 (MQ=255)
                                                                              cccATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGATCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGGTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGt                                                       <  6:425864/139‑1 (MQ=255)
                                                                                cATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑gt                                                    <  6:75606/139‑2 (MQ=255)
                                                                                           tCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGTGGGCGTTTTTggg                                          >  8:309277/1‑138 (MQ=255)
                                                                                             cAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGt                                        <  7:75501/138‑1 (MQ=255)
                                                                                                  cTTCCAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGc                                   <  3:5828/138‑1 (MQ=255)
                                                                                                     ccAATCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GGGCGTTTTTGGGTCTgggcg                                 >  6:177948/1‑134 (MQ=255)
                                                                                                        aTCGTTATTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCa                            <  3:168391/139‑1 (MQ=255)
                                                                                                              aTTTTCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTg                      <  3:251976/139‑1 (MQ=255)
                                                                                                               ttttCAACTACGAGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGGCTTTATCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGGCTGGCAAGCTCAAAATTg                      <  8:60014/138‑1 (MQ=255)
                                                                                                                     actacgaGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCtt               <  1:76207/136‑1 (MQ=255)
                                                                                                                      ctacgaGAGCAATTGGCGAACCTAGTGTCCGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCCTGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTtc              <  8:322929/137‑1 (MQ=255)
                                                                                                                      ctacgaGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTGTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTAGTTTTTGGAGTCTGGCAAGCTCAAAATTGATATCTtc              <  1:295233/137‑1 (MQ=255)
                                                                                                                      ctacgaGAGCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTtc              <  5:314458/137‑1 (MQ=255)
                                                                                                                           agagCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCg         <  4:400046/139‑1 (MQ=255)
                                                                                                                           agagCAATTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCg         <  8:423394/139‑1 (MQ=255)
                                                                                                                                 aTTGGCGAACCGAGTGTACGTGCATGGCGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGt   <  3:276453/139‑1 (MQ=255)
                                                                                                                                  ttGGCGAACCGCGTGTACGTGACTGGCGCACCCCGCTCATAATTTTTGCCTGGTCTTTTTCTATCTGCATGCGGCGGCCGCGGCCGT‑GTCCTTTTTGTCGTCTGGGAAGCTCAAAATTGATATCTTCCTCCGTTATGTa  <  6:436314/139‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                       
AAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATTTGGCGCTTCATTTCCTTTTCTTCATCCTCTGTAATCGGAGCCGCACCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACGACGAGAGCAATTGGTGAACCGAGTGTTCGTGCATGACGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GGCCTTTTTGGCGTCTGGCAAGCTCAAAATTGATATCTTCCTCCGTTATGTA  >  CP006881/2197794‑2198062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A