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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 834,206 C→G 20.1% V888V (GTC→GTG) ‡ narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE834,2060CG20.1% 121.6 / 24.5 60V888V (GTC→GTG) ‡narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base C (25/22);  new base G (7/5);  total (32/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GGATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAAT  >  minE/834137‑834271
                                                                     |                                                                 
ggATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCg                                                                  >  1:3828412/1‑71 (MQ=255)
        aaGACTGTAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAgcgc                                                          <  1:2203861/71‑1 (MQ=255)
         aGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAgcgc                                                          >  1:3061287/1‑70 (MQ=255)
           aCTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGAt                                                       <  1:1542809/71‑1 (MQ=255)
               gAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTa                                                     <  1:3722169/69‑1 (MQ=255)
               gAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTAt                                                    <  1:1140874/70‑1 (MQ=255)
               gAAAAAAGGCGAGTGCGACCAGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTa                                                     <  1:3300199/69‑1 (MQ=255)
                aaaaaaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTa                                                     <  1:1007052/68‑1 (MQ=255)
                 aaaaaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTa                                                     <  1:2411981/67‑1 (MQ=255)
                 aaaaaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTa                                                     <  1:2253779/67‑1 (MQ=255)
                 aaaaaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTa                                                     <  1:1219952/67‑1 (MQ=255)
                  aaaaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTAGt                                                                 <  1:549649/54‑1 (MQ=255)
                    aaGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTag                                                               >  1:1314382/1‑54 (MQ=255)
                      ggCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGAc                                            >  1:296099/1‑71 (MQ=255)
                      ggCGAATGCGATCTGATTCCAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTAc                                            <  1:834024/71‑1 (MQ=255)
                       gCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACt                                           <  1:3167794/71‑1 (MQ=255)
                        cGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACtt                                          <  1:3174812/71‑1 (MQ=255)
                           gTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTAc                                        >  1:92043/1‑70 (MQ=255)
                            tGCGATCTGATTCCAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGa                                      <  1:3664380/71‑1 (MQ=255)
                               gACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTAc                                        <  1:2486990/66‑1 (MQ=255)
                                 ccTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTa                                                                <  1:588364/40‑1 (MQ=255)
                                 ccTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCt                                 >  1:953478/1‑71 (MQ=255)
                                  cTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCtt                                <  1:2009306/71‑1 (MQ=255)
                                   tGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCtt                                >  1:1517072/1‑70 (MQ=255)
                                    gATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTa                              >  1:2449633/1‑71 (MQ=255)
                                     attccAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCtt                                <  1:2850084/65‑1 (MQ=255)
                                     attccAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTAc                             >  1:1821970/4‑71 (MQ=255)
                                     aTCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAgc                                                            <  1:2495032/40‑1 (MQ=255)
                                     aTCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTAc                             <  1:600680/71‑1 (MQ=255)
                                      ttccAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTAcc                            >  1:1029086/3‑71 (MQ=255)
                                      ttccAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTAcc                            >  1:3436047/3‑71 (MQ=255)
                                      ttccAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTAcc                            <  1:708956/69‑1 (MQ=255)
                                       tccAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACct                           >  1:198545/2‑71 (MQ=255)
                                        ccAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCgg                                                >  1:1851382/1‑49 (MQ=255)
                                        ccAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAAc                                    <  1:223077/61‑1 (MQ=255)
                                         cAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACctc                          >  1:1208483/1‑70 (MQ=255)
                                         cAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACctcg                         >  1:1074586/1‑70 (MQ=255)
                                         cAGGCAAAACCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACctcg                         >  1:2751193/1‑70 (MQ=255)
                                          aGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGc                                               <  1:1726855/48‑1 (MQ=255)
                                          aGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGaa                                     >  1:388248/1‑58 (MQ=255)
                                          aGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTAc                             >  1:3209724/1‑66 (MQ=255)
                                          aGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTa                        >  1:378712/1‑71 (MQ=255)
                                          aGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTa                        >  1:3951602/1‑71 (MQ=255)
                                           ggTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTAt                       >  1:3084154/1‑71 (MQ=255)
                                            gTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACt                                           >  1:799961/1‑50 (MQ=255)
                                              aaaaCCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCgg                    <  1:19573/71‑1 (MQ=255)
                                              aaaaCCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCgg                    >  1:2444626/1‑71 (MQ=255)
                                               aaaCCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGc                   >  1:1980575/1‑71 (MQ=255)
                                               aaaCCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGc                   >  1:186387/1‑71 (MQ=255)
                                                aaCCGCGCCGAATATTGTGGCGGTGGAGCGCGACTACCCTGCTACGTATGAACGCTTTACCTCGCTCgggc                  >  1:1391442/1‑69 (MQ=255)
                                                 aCCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACt                                           <  1:3739987/45‑1 (MQ=255)
                                                 aCCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGccc                 <  1:2561972/71‑1 (MQ=255)
                                                  ccGCGCCACACATTATGGTCGTAGAGCGCGATTATca                                                  >  1:1461547/1‑36 (MQ=255)
                                                   cgcgCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCg                >  1:1932590/1‑70 (MQ=255)
                                                    gcgcCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCt              >  1:1281191/1‑71 (MQ=255)
                                                        cacacaTTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGAt           <  1:3158329/70‑1 (MQ=255)
                                                          cacaTTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATg          >  1:2937784/1‑69 (MQ=255)
                                                               tATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTa                              >  1:2014898/1‑44 (MQ=255)
                                                                aTGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAAt  >  1:320999/1‑71 (MQ=255)
                                                                  ggTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACctct                         <  1:3806373/46‑1 (MQ=255)
                                                                     |                                                                 
GGATGTGAAAGACTGGAAAAAAGGCGAGTGCGACCTGATCCCAGGTAAAACCGCGCCACACATTATGGTCGTAGAGCGCGATTATCCGGCGACTTACGAACGCTTTACCTCTATCGGCCCGCTGATGGAGAAAAT  >  minE/834137‑834271

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A