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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,656,211 T→C 46.0% I566I (ATT→ATC)  glgP → glycogen phosphorylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,656,2110TC46.0% 14.7 / 104.7 123I566I (ATT→ATC) glgPglycogen phosphorylase
Reads supporting (aligned to +/- strand):  ref base T (34/32);  new base C (24/32);  total (59/64)
Fisher's exact test for biased strand distribution p-value = 3.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

Only 100 of 130 total aligned reads displayed.

TTGTTCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTTTGGCG  >  minE/2656143‑2656278
                                                                    |                                                                   
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:1042768/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:327577/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:2147077/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:1207613/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:121357/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:3300482/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:1978269/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:2412141/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    <  1:457376/69‑1 (MQ=255)
  gttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                                    >  1:1212521/1‑68 (MQ=255)
  gttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTAc                                                                   >  1:3192041/1‑69 (MQ=255)
  gttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTAc                                                                   >  1:2161780/1‑69 (MQ=255)
          tACAAATCAAACGTATTCACTAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCtata                                                           <  1:577260/69‑1 (MQ=255)
          tACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCtata                                                           <  1:180311/69‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGACTGTGTTGCACGTGATCACCCTCTATaa                                                          <  1:442241/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:2439797/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:2618100/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:2628021/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:2347749/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:296178/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:1768443/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:2254666/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:1639462/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:1633065/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:372226/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                          <  1:1442086/68‑1 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATTACCCGCTATAAc                                                         >  1:280355/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCtatagc                                                         >  1:2962273/1‑66 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:401804/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:2172292/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:791187/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:646864/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:1259655/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:2014448/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:1415962/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:1647940/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                         >  1:3228156/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATAAca                                                                  >  1:53073/1‑58 (MQ=255)
                 cAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCtata                                                           >  1:3192865/1‑62 (MQ=255)
                 cAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCtata                                                           >  1:1068608/1‑62 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:2225939/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:1276482/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:485473/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:378121/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:1176605/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:1602350/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:3074076/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:186763/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:2830142/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:1909968/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:2610583/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                                 <  1:2107259/69‑1 (MQ=255)
                         ttCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:1523978/1‑69 (MQ=255)
                         ttCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:2258648/1‑69 (MQ=255)
                           cACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGAtt                                                                     >  1:233608/1‑42 (MQ=255)
                           cACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGAc                                          >  1:533750/1‑69 (MQ=255)
                              gAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCg                                       <  1:1449947/69‑1 (MQ=255)
                              gAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCg                                       <  1:3098594/69‑1 (MQ=255)
                              gAATACAAACGTCAATTGATGAATGTGTT‑CATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCg                                       <  1:1323575/68‑1 (MQ=255)
                                aTACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGa                                     <  1:234859/69‑1 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                                    >  1:459403/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                                    >  1:1392433/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                                    >  1:2418248/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                                    >  1:1097852/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                                    >  1:1735114/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                                    >  1:2212109/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                                    >  1:3112800/1‑69 (MQ=255)
                                   cAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATg                                   >  1:31066/1‑68 (MQ=255)
                                   cAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATAAAGGCCGACCCGGATg                                   >  1:311357/1‑68 (MQ=255)
                                   cAAACGTCAATTGACGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATg                                   >  1:76969/1‑68 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             <  1:2127110/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             <  1:881777/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             <  1:587544/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             <  1:1656353/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             <  1:1972781/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             <  1:2716064/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             <  1:189386/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             <  1:2829832/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTAcc                      >  1:2780510/1‑69 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTAcc                      >  1:2755210/1‑69 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTAcc                      >  1:2400974/1‑69 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                             >  1:2561913/1‑42 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:3372241/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:72654/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:1431404/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:32940/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:1389388/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:3014213/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:3265027/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                            >  1:92096/1‑43 (MQ=255)
                                                      gtgtTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg               <  1:2231696/69‑1 (MQ=255)
                                                      gtgtTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg               <  1:1607772/69‑1 (MQ=255)
                                                           gCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg               <  1:2552424/64‑1 (MQ=255)
                                                           gCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg               <  1:24753/64‑1 (MQ=255)
                                                              tgtgATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg               <  1:332990/61‑1 (MQ=255)
                                                                    tACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTTTGGCg  >  1:1568986/1‑68 (MQ=255)
                                                                    tACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTTTGGCg  >  1:663683/1‑68 (MQ=255)
                                                                    tACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTTTGGCg  >  1:2700269/1‑68 (MQ=255)
                                                                    tACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTTTGGCg  >  1:1941556/1‑68 (MQ=255)
                                                                    tACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTTTGGCg  >  1:954103/1‑68 (MQ=255)
                                                                    |                                                                   
TTGTTCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTTTGGCG  >  minE/2656143‑2656278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A