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 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,880,549 T→C T71A (ACC→GCC)  leuE ← leucine efflux protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,880,5490TC98.2% 186.5 / ‑6.0 55T71A (ACC→GCC) leuEleucine efflux protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (26/28);  total (27/28)
Fisher's exact test for biased strand distribution p-value = 4.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTC  >  NC_000913/1880458‑1880640
                                                                                           |                                                                                           
cccTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaatta                                                                                     >  1:788118/1‑100 (MQ=255)
  cTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTtaattaat                                                                                   >  1:653735/1‑100 (MQ=255)
     cAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATg                                                                                  >  2:1568520/1‑98 (MQ=255)
        ggTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGcc                                                                             <  1:1082589/100‑1 (MQ=255)
           cgcgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACt                                                                          >  1:1321114/1‑100 (MQ=255)
             cgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATATCACGACTcc                                                                        >  2:463220/1‑100 (MQ=255)
               tAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAg                                                                      <  1:1373197/100‑1 (MQ=255)
               tAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAg                                                                      >  1:240213/1‑100 (MQ=255)
                aaaGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAga                                                                     >  2:1373190/1‑99 (MQ=255)
                aaaGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGc                                                                     >  1:489569/1‑100 (MQ=255)
                     aTTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATg                                                                >  2:983501/1‑100 (MQ=255)
                     aTTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATg                                                                <  1:903135/100‑1 (MQ=255)
                       tttACTCCCCAGATAGAGCAAATAAAACGCAGCAAGATCACATACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGc                                                               <  2:1108086/99‑1 (MQ=255)
                        ttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCa                                                             <  1:1132005/100‑1 (MQ=255)
                          ccgatctaGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGa                                                           <  1:441834/93‑1 (MQ=255)
                           cTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaa                                                          >  2:1130848/1‑100 (MQ=255)
                           cTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTCATTAATGTCGCCACTCCAGCCCATGCCAGaa                                                          >  2:1516547/1‑100 (MQ=255)
                            tCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaaa                                                         <  2:511019/100‑1 (MQ=255)
                            tCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaaa                                                         >  2:1241740/1‑100 (MQ=255)
                            tCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaa                                                          <  2:1299496/99‑1 (MQ=255)
                            tCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTAGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaaa                                                         >  2:1201227/1‑100 (MQ=255)
                             ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAAc                                                        >  1:459215/1‑100 (MQ=255)
                             ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAAc                                                        <  1:501100/100‑1 (MQ=255)
                             ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAAc                                                        <  2:1324789/100‑1 (MQ=255)
                             ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCAATGCCAGAAAc                                                        <  2:1408479/100‑1 (MQ=255)
                                cAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATc                                                     <  2:467538/100‑1 (MQ=255)
                                 aGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaagatcgg                                                    >  2:441833/1‑94 (MQ=255)
                                 aGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATc                                                     <  2:873931/99‑1 (MQ=255)
                                  gATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCaa                                                   >  1:873060/1‑100 (MQ=255)
                                    tAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATa                                                 >  1:1005735/1‑100 (MQ=255)
                                        gCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGc                                             >  2:893249/1‑100 (MQ=255)
                                         cAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCa                                            >  1:538679/1‑100 (MQ=255)
                                           aaTAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATc                                          >  1:1368048/1‑100 (MQ=255)
                                              aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                       <  1:1516556/100‑1 (MQ=255)
                                              aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                       <  1:84464/100‑1 (MQ=255)
                                               aaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCa                                      >  1:510182/1‑100 (MQ=255)
                                               aaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCa                                      >  1:855297/1‑100 (MQ=255)
                                                  cGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaata                                   <  2:700442/100‑1 (MQ=255)
                                                  cGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCAATCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaat                                    >  1:389274/1‑99 (MQ=255)
                                                  cGCACCAAGATAACGTACAATGTTGAATAATATCAGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaata                                   <  2:1290352/100‑1 (MQ=255)
                                                     aCCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaataaat                                <  2:485369/100‑1 (MQ=255)
                                                        aaGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATaca                             <  2:378397/100‑1 (MQ=255)
                                                            tAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGc                         <  1:2998/100‑1 (MQ=255)
                                                             aaCGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCGATAAATACACCGCa                        <  2:811324/100‑1 (MQ=255)
                                                                gTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGc                     >  1:604726/1‑100 (MQ=255)
                                                                 tACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGcc                    >  1:1374612/1‑100 (MQ=255)
                                                                    aaTGTTGAATAATATCGGGGTGGCCTTAATTAAAGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCa                 <  2:51688/100‑1 (MQ=255)
                                                                         tGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATa            >  2:163040/1‑100 (MQ=255)
                                                                         tGAATAAGATCGGGGTGGCCTTAATTAATGTCGATCCTCCAGCCCATGCCAGAAACAACAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAg               <  2:273543/97‑1 (MQ=255)
                                                                           aataatATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAAc          >  2:1097273/1‑100 (MQ=255)
                                                                            ataataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAAcc         <  2:1360843/100‑1 (MQ=255)
                                                                             taataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCg        <  1:1241745/100‑1 (MQ=255)
                                                                              aataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGc       <  2:788113/100‑1 (MQ=255)
                                                                                 atCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCtt    <  1:91472/100‑1 (MQ=255)
                                                                                   cGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTc  <  1:1436338/100‑1 (MQ=255)
                                                                                           |                                                                                           
CCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTC  >  NC_000913/1880458‑1880640

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A