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 2,656,205 T→C 47.9% H564H (CAT→CAC)  glgP → glycogen phosphorylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,656,2050TC47.9% 1.7 / 110.6 121H564H (CAT→CAC) glgPglycogen phosphorylase
Reads supporting (aligned to +/- strand):  ref base T (32/31);  new base C (26/32);  total (58/63)
Fisher's exact test for biased strand distribution p-value = 5.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

Only 100 of 125 total aligned reads displayed.

TTGTTCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTT  >  minE/2656143‑2656273
                                                              |                                                                    
ttgttCGATGTA‑AAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:3288247/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:863105/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:1207613/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:121357/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:457376/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:2147077/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:327577/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:1978269/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:1042768/69‑1 (MQ=255)
 tgttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               <  1:2412141/69‑1 (MQ=255)
  gttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTa                                                               >  1:1212521/1‑68 (MQ=255)
  gttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTAc                                                              >  1:3192041/1‑69 (MQ=255)
  gttCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTAc                                                              >  1:2161780/1‑69 (MQ=255)
          tACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCtata                                                      <  1:180311/69‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGACTGTGTTGCACGTGATCACCCTCTATaa                                                     <  1:442241/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:1768443/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:296178/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:372226/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:2254666/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:2347749/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:2423248/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:3202636/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:3109209/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:2618100/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:2628021/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:1442086/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:1436155/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:1633065/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:1228675/68‑1 (MQ=255)
            cAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATaa                                                     <  1:1639462/68‑1 (MQ=255)
             aaaTCAAACGTATTCTCGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:2770093/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATTACCCGCTATAAc                                                    >  1:280355/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCtatagc                                                    >  1:2962273/1‑66 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:1647940/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:2014448/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:401804/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:791187/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:1415962/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:2161133/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:646864/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAAc                                                    >  1:2172292/1‑68 (MQ=255)
             aaaTCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATAAca                                                             >  1:53073/1‑58 (MQ=255)
                 cAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCtata                                                      >  1:1068608/1‑62 (MQ=255)
                 cAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCtata                                                      >  1:3192865/1‑62 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:485473/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:2225939/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:2219013/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:3074076/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:1602350/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:688697/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:2107259/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:1176605/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:1276482/69‑1 (MQ=255)
                    aCGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:1909968/69‑1 (MQ=255)
                     cGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCGCTATAACCGCATCaa                                            <  1:1833871/68‑1 (MQ=255)
                         ttCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:1523978/1‑69 (MQ=255)
                           cACGAATACAAACGTCAATTGATGAATGTGTTGCAtgt                                                                    >  1:1869177/1‑38 (MQ=255)
                           cACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGAtt                                                                >  1:233608/1‑42 (MQ=255)
                           cACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGAc                                     >  1:533750/1‑69 (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                               >  1:559320/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                               >  1:2418248/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                               >  1:1097852/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                               >  1:1932750/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                               >  1:1735114/1‑69 (MQ=255)
                                 tACAAACGTCAATTGATGAATGTGTTGCACGTGATCACCCACTATAACCGCATCAAGGCCGACCCGGAt                               >  1:2597940/1‑69 (MQ=255)
                                   cAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATg                              >  1:31066/1‑68 (MQ=255)
                                   cAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATg                              >  1:2076636/1‑68 (MQ=255)
                                   cAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATAAAGGCCGACCCGGATg                              >  1:311357/1‑68 (MQ=255)
                                         tCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTg                       >  1:2671201/1‑69 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                        <  1:2829832/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                        <  1:2716064/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                        <  1:189386/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                        <  1:1656353/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                        <  1:587544/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                        <  1:881777/46‑1 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTAcc                 >  1:2400974/1‑69 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTAcc                 >  1:2780510/1‑69 (MQ=255)
                                               gatgaATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTAcc                 >  1:2854603/1‑69 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGcc                                        >  1:2561913/1‑42 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:72654/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:1389388/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:1431404/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:1344632/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:92096/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:3372241/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:32940/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:2304000/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:3265027/1‑43 (MQ=255)
                                                   aaTGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCg                                       >  1:3014213/1‑43 (MQ=255)
                                                      gtgtTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg          <  1:2231696/69‑1 (MQ=255)
                                                      gtgtTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg          <  1:1607772/69‑1 (MQ=255)
                                                           gCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg          <  1:430324/64‑1 (MQ=255)
                                                           gCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg          <  1:1561206/64‑1 (MQ=255)
                                                           gCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg          <  1:24753/64‑1 (MQ=255)
                                                           gCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg          <  1:2552424/64‑1 (MQ=255)
                                                              tgtgATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTg          <  1:332990/61‑1 (MQ=255)
                                                              tgtgATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATAtttt  >  1:3356344/1‑69 (MQ=255)
                                                              |                                                                    
TTGTTCGATGTACAAATCAAACGTATTCACGAATACAAACGTCAATTGATGAATGTGTTGCATGTGATTACCCGCTATAACCGCATCAAGGCCGACCCGGATGCGAAGTGGGTACCGCGCGTGAATATTTT  >  minE/2656143‑2656273

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