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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,042,482 C→T 15.8% M57I (ATG→ATA)  glgS ← predicted glycogen synthesis protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,042,4820CT15.8% 291.6 / 40.9 114M57I (ATG→ATA) glgSpredicted glycogen synthesis protein
Reads supporting (aligned to +/- strand):  ref base C (51/44);  new base T (4/14);  total (55/59)
Fisher's exact test for biased strand distribution p-value = 1.97e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

Only 100 of 120 total aligned reads displayed.

TAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGTTAC  >  minE/2042414‑2042549
                                                                    |                                                                   
tAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGcat                                                                   >  1:1752539/1‑71 (MQ=255)
  aTACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGtatca                                                                 >  1:816104/1‑71 (MQ=255)
     cAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCt                                                              >  1:3317205/1‑71 (MQ=255)
       aaCACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCt                                                              >  1:1841177/1‑69 (MQ=255)
        acacTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGtt                                                           <  1:1610759/71‑1 (MQ=255)
         cacTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTg                                                             >  1:3201975/1‑68 (MQ=255)
           cTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:2267727/71‑1 (MQ=255)
              aaaCGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACaa                                                      <  1:3465688/70‑1 (MQ=255)
              aaaCGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACaa                                                      <  1:2230153/70‑1 (MQ=255)
                     ccATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAAt                                                     <  1:2877619/64‑1 (MQ=255)
                       aTCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTg                                                             <  1:1807779/54‑1 (MQ=255)
                        tCAGGCCCGTTATATCAGTTCTCTAACTCCAGCTCTCTTGCCTGcatc                                                                  <  1:3634078/48‑1 (MQ=255)
                         cAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:3185128/57‑1 (MQ=255)
                         cAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATaa                                          >  1:3049781/1‑71 (MQ=255)
                          aGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGTATCATCTGTTGACaa                                                      >  1:3739365/1‑58 (MQ=255)
                          aGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGTATCATCTGTTGACAAt                                                     <  1:1038219/59‑1 (MQ=255)
                          aGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGTATCATCTGTTGACAAt                                                     <  1:819646/59‑1 (MQ=255)
                          aGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCt                                                              >  1:3519433/1‑50 (MQ=255)
                          aGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAAc                                         >  1:3438963/1‑71 (MQ=255)
                          aGGCCCGTTATATCAGTGCTCTAACTACAGCTCTCTTGCCTGTATCATCTGTTGACAATACCAGGCATAAc                                         >  1:2603747/1‑71 (MQ=255)
                             cccGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:1705303/53‑1 (MQ=255)
                             cccGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTg                                      <  1:1308834/71‑1 (MQ=255)
                               cGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGcatcat                                                                >  1:2383382/1‑43 (MQ=255)
                                gTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:2637337/50‑1 (MQ=255)
                                gTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTgcg                                    >  1:1147873/1‑70 (MQ=255)
                                gTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTgcg                                    >  1:3710426/1‑70 (MQ=255)
                                gTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTgcg                                    >  1:404965/1‑70 (MQ=255)
                                 ttATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGTATCATCTGTTg                                                          <  1:3153653/47‑1 (MQ=255)
                                 ttATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACaa                                                      <  1:59436/51‑1 (MQ=255)
                                 ttATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTgcgc                                   >  1:358091/1‑70 (MQ=255)
                                   atatCAGTGCTCTAACTCCAGCTCTCTTGCCTGTATCATCTGTTGACAAt                                                     >  1:3734700/1‑50 (MQ=255)
                                   atatCAGTGCTCTAACTCCAGCTCTCTTGCCTGTATCATCTGTTGACAATACCAGGCATAACGTGCGCaa                                 <  1:347157/70‑1 (MQ=255)
                                   atatCAGTGCTCTAACTCCAGCTCTCTTGCCTGTATCATCTGTTGACAATACCAGGCATAACGTGCGCaa                                 <  1:1347729/70‑1 (MQ=255)
                                   atatCAGTGCTCTAACTCCAGCTCTCTTGCCTGTATCATCTGTTGACAATACCAGGCATAACGTGCGCaa                                 <  1:3363248/70‑1 (MQ=255)
                                   atatCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaa                                 <  1:1489803/70‑1 (MQ=255)
                                   atatCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaa                                 >  1:3138263/1‑70 (MQ=255)
                                   atatCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaa                                 <  1:1559952/70‑1 (MQ=255)
                                   atatCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaa                                 >  1:1722765/1‑70 (MQ=255)
                                   atatCAGTGCTCTAACT‑CAGCTCTCTTGCCTGTATCATCTGTTGACAAt                                                     >  1:2721989/1‑49 (MQ=255)
                                    tatCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:3686502/46‑1 (MQ=255)
                                    tatCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:2071720/46‑1 (MQ=255)
                                    tatCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaaaa                               >  1:863682/1‑71 (MQ=255)
                                    tatCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaaaa                               >  1:88305/1‑71 (MQ=255)
                                     atCAGTGCTCTAACTCCAGCTCTCTTGCCTGAATCATCTGTTGACAATACCAGGCATaa                                          <  1:211443/59‑1 (MQ=255)
                                      tCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGtt                                                           <  1:3618504/41‑1 (MQ=255)
                                      tCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:405854/44‑1 (MQ=255)
                                      tCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:2318086/44‑1 (MQ=255)
                                      tCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAAc                              >  1:1035779/1‑70 (MQ=255)
                                      tCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAAc                              <  1:4025800/70‑1 (MQ=255)
                                       cAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGa                                                         >  1:2108764/1‑42 (MQ=255)
                                          tGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGt                         >  1:3818524/1‑71 (MQ=255)
                                            ctctAACTCCAGCTCTCTTGCCTGTATCATCTGTTGAc                                                        <  1:823698/38‑1 (MQ=255)
                                            ctctAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATa                                                    >  1:3035914/1‑42 (MQ=255)
                                            ctctAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAg                                                <  1:2292030/46‑1 (MQ=255)
                                            ctctAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTc                       <  1:51704/71‑1 (MQ=255)
                                               tAACTCCAGCTCTCTTGCCTGTATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCt                      <  1:2174524/69‑1 (MQ=255)
                                               tAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:580360/35‑1 (MQ=255)
                                               tAACTCCAGCTCTCTTGCCTGCATCATCTGTTGAc                                                        <  1:2443687/35‑1 (MQ=255)
                                               tAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCTCAAAACCAGGTTCTAt                    >  1:171762/1‑71 (MQ=255)
                                               tAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCt                      <  1:2744008/69‑1 (MQ=255)
                                               tAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTAt                    >  1:2241366/1‑71 (MQ=255)
                                                aaCTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATg                   >  1:3311604/1‑71 (MQ=255)
                                                 aCTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTTCGCAAAACCAGGTTCTATGt                  >  1:2005613/1‑71 (MQ=255)
                                                 aCTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGt                  >  1:1691112/1‑71 (MQ=255)
                                                 aCTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGt                  >  1:260657/1‑71 (MQ=255)
                                                 aCTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGt                  >  1:1575802/1‑71 (MQ=255)
                                                 aCTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGt                  >  1:3272646/1‑71 (MQ=255)
                                                    ccAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCa                            >  1:1393280/1‑58 (MQ=255)
                                                    ccAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGttct               >  1:4102735/1‑71 (MQ=255)
                                                     cAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATaa                                          >  1:2611918/1‑43 (MQ=255)
                                                     cAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGttc                <  1:1562404/69‑1 (MQ=255)
                                                        ctctctTGCCTGCATCATCTGTTGACAATACCAGGCATaa                                          <  1:250757/40‑1 (MQ=255)
                                                        ctctctTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTc                       <  1:1528218/59‑1 (MQ=255)
                                                        ctctctTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCAt           >  1:3270338/1‑71 (MQ=255)
                                                        ctctctTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCAt           >  1:1930686/1‑71 (MQ=255)
                                                         tctctTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaaaa                               >  1:2879584/1‑50 (MQ=255)
                                                          ctctTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATc          >  1:2812147/1‑70 (MQ=255)
                                                          ctctTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATc          >  1:1215859/1‑70 (MQ=255)
                                                           tctTGCCTGTATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATc          <  1:437665/69‑1 (MQ=255)
                                                           tctTGCCTGCATCATCTGTTGACAATACCAGGCAt                                            <  1:2838244/35‑1 (MQ=255)
                                                             ttGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaaaa                               >  1:2973904/1‑46 (MQ=255)
                                                             ttGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGttct               >  1:3936636/1‑62 (MQ=255)
                                                             ttGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCa            >  1:499910/1‑65 (MQ=255)
                                                             ttGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATg      >  1:1302707/1‑71 (MQ=255)
                                                             ttGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTAATCCATg      >  1:2915506/1‑71 (MQ=255)
                                                             ttGCCTGCATCATCTGTTGA‑AATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCa            >  1:2662049/1‑64 (MQ=255)
                                                              tGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGt     >  1:2465733/1‑71 (MQ=255)
                                                               gCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGt     >  1:267887/1‑70 (MQ=255)
                                                               gCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGt     >  1:1373500/1‑70 (MQ=255)
                                                                ccTGTATCATCTGTTGACAATACCAGGCATAACGTGCGCaaa                                <  1:3209863/42‑1 (MQ=255)
                                                                ccTGTATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCAt       <  1:1790456/67‑1 (MQ=255)
                                                                ccTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGTTa   <  1:3082801/71‑1 (MQ=255)
                                                                 cTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGTTAc  <  1:3002634/71‑1 (MQ=255)
                                                                 cTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGTTAc  <  1:1124749/71‑1 (MQ=255)
                                                                 cTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGTTAc  <  1:2639641/71‑1 (MQ=255)
                                                                  tGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaaa                                <  1:515530/40‑1 (MQ=255)
                                                                  tGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaaa                                <  1:3974694/40‑1 (MQ=255)
                                                                  tGCATCATCTGTTGACAATACCAGGCATAACGTGCGCaaa                                <  1:3511619/40‑1 (MQ=255)
                                                                   gCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGTTAc  >  1:3085331/1‑69 (MQ=255)
                                                                    catcatCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGt     <  1:249015/65‑1 (MQ=255)
                                                                    |                                                                   
TAATACAAACACTAAAACGGGCCATCAGGCCCGTTATATCAGTGCTCTAACTCCAGCTCTCTTGCCTGCATCATCTGTTGACAATACCAGGCATAACGTGCGCAAAACCAGGTTCTATGTTCTTCATCCATGTTAC  >  minE/2042414‑2042549

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