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 2,197,913 G→T V75V (GTC→GTA)  U712_11010 ← Chorismate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068812,197,9130GT93.8% 132.1 / ‑6.1 48V75V (GTC→GTA) U712_11010Chorismate synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (15/30);  minor base A (3/0);  total (18/30)
Fisher's exact test for biased strand distribution p-value = 4.72e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTAATCGCTCCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATTTGGCGCTTCATTTCCTTTTCTTCATCCTCTGTAATCGGAGCCGCACCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACGACGAGAGCAATTGGTGAACCGAGTGTTCGTGCATGACGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GGCCTTTTTGGCGTCTGGCAAGCTCAAAATTG  >  CP006881/2197778‑2198042
                                                                                                                                       |                                                                                                                                  
tttAATTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTGTTCATCTTCTGTTATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCCATCGTTTTTTTCAactacg                                                                                                                                 >  5:75066/1‑139 (MQ=255)
   aaTTGCACCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTTTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAActacga                                                                                                                                >  6:314458/1‑137 (MQ=255)
        caccGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATATTCTGTAATCGGAGCGGGGCCCATGATTTTTGTGGAATTCGTGCAAACGTTTTTTTAAACTTCGACTGCAAt                                                                                                                         >  2:76207/3‑139 (MQ=255)
           cGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTgg                                                                                                                      <  4:183477/139‑1 (MQ=255)
           cGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCTTTTCTTCATCTTCTGTAATCGGAGCGGCGCCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACTACGAGAGCAATTgg                                                                                                                      <  5:263872/139‑1 (MQ=255)
             tttAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATCTGGCGCTTCATTTCCATTTCTTCATCATCTGTAATAGGAGCGGCGCCCAAGATTTTTTTGCAATGCTTCCAATCCTTATTTTCAACAACTAGAGCAATTggc                                                                                                                     >  6:186526/1‑137 (MQ=255)
                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)
                                                                                                                                       |                                                                                                                                  
TTTAATCGCTCCGTTTAAGTCAGCGTGCCCAGGTCTCGGTCTGGAAATTTGGCGCTTCATTTCCTTTTCTTCATCCTCTGTAATCGGAGCCGCACCCATGATTTTTGTCCAATGCTTCCAATCGTTATTTTCAACGACGAGAGCAATTGGTGAACCGAGTGTTCGTGCATGACGCACCCCGCTCATAATTTTGGCCTGGTCTTTTTCGATCTGCATGCGGCGGCCGCGGCCGT‑GGCCTTTTTGGCGTCTGGCAAGCTCAAAATTG  >  CP006881/2197778‑2198042

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