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 706,680 C→T 48.3% R244K (AGG→AAG)  lpxL ← lauryl‑acyl carrier protein (ACP)‑dependent acyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE706,6800CT48.3% 3.9 / 80.0 60R244K (AGG→AAG) lpxLlauryl‑acyl carrier protein (ACP)‑dependent acyltransferase
Reads supporting (aligned to +/- strand):  ref base C (14/17);  new base T (17/12);  total (31/29)
Fisher's exact test for biased strand distribution p-value = 3.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCATCATCCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGTTCCGGTCGTGGT  >  minE/706613‑706750
                                                                   |                                                                      
ggCATCATCCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTa                                                                      <  1:155364/70‑1 (MQ=255)
ggCATCATCCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTAc                                                                     >  1:667509/1‑71 (MQ=255)
ggCATCATCCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTa                                                                      >  1:1902880/1‑70 (MQ=255)
   atcatcCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGc                                                                  <  1:3713973/71‑1 (MQ=255)
   atcatcCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGc                                                                  <  1:3179163/71‑1 (MQ=255)
       tcCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTgg                                                              <  1:3051373/71‑1 (MQ=255)
       tcCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTg                                                               >  1:1400883/1‑70 (MQ=255)
         cAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGaa                                                            >  1:2090058/1‑71 (MQ=255)
          aGTGGCGGAGAACACTCTGGCGTCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAAc                                                           <  1:3832297/71‑1 (MQ=255)
          aGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAAc                                                           >  1:2166284/1‑71 (MQ=255)
          aGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAAc                                                           <  1:2280555/71‑1 (MQ=255)
           gTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACg                                                          <  1:314330/71‑1 (MQ=255)
            tGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGa                                                         <  1:64875/71‑1 (MQ=255)
            tGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGc                                                                  <  1:3102492/62‑1 (MQ=255)
            tGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGa                                                         <  1:2457902/71‑1 (MQ=255)
              gCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACg                                                          >  1:2756922/1‑68 (MQ=255)
              gCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGaa                                                        <  1:3648848/70‑1 (MQ=255)
                ggAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGa                                                             <  1:2857560/63‑1 (MQ=255)
                 gagaACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGc                                                                  <  1:3493556/57‑1 (MQ=255)
                 gagaACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGc                                                                  <  1:1021251/57‑1 (MQ=255)
                   gaACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCAc                                                  >  1:3378801/1‑71 (MQ=255)
                      cacTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGaa                                                        >  1:1119403/1‑62 (MQ=255)
                      cacTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAg                                               <  1:796941/71‑1 (MQ=255)
                        ctctGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGa                                              >  1:3093766/1‑70 (MQ=255)
                         tctGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGc                                                                  >  1:79990/1‑49 (MQ=255)
                           tGGCGGCAGCATAATCAATTGATACCTTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATg                                          >  1:1423311/1‑71 (MQ=255)
                           tGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGa                                                         <  1:3325833/56‑1 (MQ=255)
                           tGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCACCAGACa                                            <  1:2599874/69‑1 (MQ=255)
                             gcggcAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCa                                                <  1:33538/63‑1 (MQ=255)
                             gcggcAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATgcg                                        >  1:538476/1‑71 (MQ=255)
                             gcggcAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATgc                                         <  1:1473593/70‑1 (MQ=255)
                                gcagcaTAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAgg                                                      <  1:2246336/54‑1 (MQ=255)
                                 cagcaTAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCAcc                                                 <  1:2916753/58‑1 (MQ=255)
                                   gcaTAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAg                                               >  1:31418/1‑58 (MQ=255)
                                     aTAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCa                                                   >  1:3049575/1‑52 (MQ=255)
                                     aTAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCa                                                   >  1:882503/1‑52 (MQ=255)
                                     aTAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCa                                                   >  1:3237078/1‑52 (MQ=255)
                                     aTAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCa                                                   >  1:3060840/1‑52 (MQ=255)
                                     aTAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCa                                                   >  1:923435/1‑52 (MQ=255)
                                     aTAATCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACAt                                <  1:2926149/71‑1 (MQ=255)
                                       aaTCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACGAAggg                                                     >  1:2058345/1‑48 (MQ=255)
                                        aTCAATTGATACCCTTTGCCATCTGGCTTACGGCGTGGAACg                                                          <  1:3200515/42‑1 (MQ=255)
                                         tCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGAc                                             <  1:1525963/54‑1 (MQ=255)
                                           aaTTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGc                                                    >  1:1650768/1‑45 (MQ=255)
                                           aaTTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGc                                                    >  1:1768887/1‑45 (MQ=255)
                                                aTACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCa                     <  1:3672643/71‑1 (MQ=255)
                                                  aCCCTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATc                   >  1:1456431/1‑71 (MQ=255)
                                                   cccTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATcc                  <  1:1136347/71‑1 (MQ=255)
                                                    ccTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATcc                  <  1:1387124/70‑1 (MQ=255)
                                                     cTTTGCCATCTGGCTTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCAt                    >  1:2922509/1‑67 (MQ=255)
                                                      tttGCCATCTGGCTTACGGCGTGGAACGAAGGGCACCAGACATgc                                         <  1:3291829/45‑1 (MQ=255)
                                                      tttGCCATCTGGCTTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAgg               >  1:615606/1‑71 (MQ=255)
                                                      tttGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAgg               >  1:3504992/1‑71 (MQ=255)
                                                        tGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGtt             >  1:2016051/1‑71 (MQ=255)
                                                         gCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGtt             <  1:939370/70‑1 (MQ=255)
                                                            aTCTGGCTTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGTTCCgg         >  1:3764908/1‑71 (MQ=255)
                                                            aTCTGGCTTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGTTCCgg         >  1:2478136/1‑71 (MQ=255)
                                                               tGGCTTACGGCGTGGAACGAAGGGCACCAGAAATGCGCCGGACATCCGTGCCAGCATCCAGGTTCCGGTCg      >  1:1609612/1‑71 (MQ=255)
                                                               tGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGTTCCGGTCg      >  1:344947/1‑71 (MQ=255)
                                                               tGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGTTCCGGTCg      >  1:1730857/1‑71 (MQ=255)
                                                                   cTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGTTCCGGTCGTGGt  >  1:3404665/1‑71 (MQ=255)
                                                                   |                                                                      
GGCATCATCCAGTGGCGGAGAACACTCTGGCGGCAGCATAATCAATTGATACCCTTTGCCATCTGGCCTACGGCGTGGAACGAAGGGCACCAGACATGCGCCGGACATCCGTGCCAGCATCCAGGTTCCGGTCGTGGT  >  minE/706613‑706750

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A