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 R2 230 93.6 4701257 96.3% 4527310 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,981,954 T→C 5.6% T41A (ACG→GCG)  yggR ← predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,981,9540TC 5.6% 192.5 / 2.9 71T41A (ACG→GCG) yggRpredicted transporter
Reads supporting (aligned to +/- strand):  ref base T (35/32);  new base C (2/2);  total (37/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.45e-01

CCATTCTCCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAG  >  minE/1981884‑1982023
                                                                      |                                                                     
ccATTCTCCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGt                                                                       <  1:2159460/71‑1 (MQ=255)
  aTTCTCCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGt                                                                       <  1:1673054/69‑1 (MQ=255)
    tctcCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATc                                                                    >  1:1381229/1‑70 (MQ=255)
     ctcCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCa                                                                   >  1:3596703/1‑70 (MQ=255)
     ctcCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCa                                                                   >  1:2491295/1‑70 (MQ=255)
     ctcCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCa                                                                   >  1:2026589/1‑70 (MQ=255)
        cAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCTACGTCCGGCGTATCaaa                                                                 <  1:1590946/69‑1 (MQ=255)
        cAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCaaa                                                                 <  1:1518193/69‑1 (MQ=255)
          gCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGgc                                                             <  1:1428433/71‑1 (MQ=255)
           cAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGgcg                                                            >  1:1494584/1‑71 (MQ=255)
           cAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGgcg                                                            >  1:3443396/1‑71 (MQ=255)
            aaTATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCaaa                                                                 >  1:2075273/1‑65 (MQ=255)
            aaTATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCaaa                                                                 >  1:4563825/1‑65 (MQ=255)
            aaTATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGgcgc                                                           <  1:3978872/71‑1 (MQ=255)
             atatTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCaaa                                                                 >  1:4357782/1‑64 (MQ=255)
             atatTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCa                                                          <  1:2845524/71‑1 (MQ=255)
               atTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGt                                                                       >  1:1235749/1‑56 (MQ=255)
               atTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCaa                                                                  <  1:2647128/61‑1 (MQ=255)
                ttGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCa                                                                   <  1:3529424/59‑1 (MQ=255)
                ttGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCt                                                       >  1:4354587/1‑71 (MQ=255)
                  gCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTAt                                                                     >  1:1239848/1‑55 (MQ=255)
                  gCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTc                                                     >  1:564475/1‑71 (MQ=255)
                     cGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCa                                                   <  1:934249/70‑1 (MQ=255)
                     cGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCAt                                                  <  1:4361197/71‑1 (MQ=255)
                     cGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCAt                                                  <  1:3338813/71‑1 (MQ=255)
                     cGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCAt                                                  <  1:757352/71‑1 (MQ=255)
                      gCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCAtt                                                 >  1:587275/1‑71 (MQ=255)
                          aTCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGgcg                                                            <  1:3126993/56‑1 (MQ=255)
                          aTCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGc                                             >  1:1352948/1‑71 (MQ=255)
                           tCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGcc                                            >  1:4269140/1‑71 (MQ=255)
                            cGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCaaa                                                                 >  1:371496/1‑49 (MQ=255)
                            cGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCcg                                           >  1:4217663/1‑71 (MQ=255)
                             gTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCAt                                                  <  1:3361978/63‑1 (MQ=255)
                             gTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCAt                                                  <  1:3356429/63‑1 (MQ=255)
                             gTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCAt                                                  <  1:292636/63‑1 (MQ=255)
                             gTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCcgc                                          >  1:1098831/1‑71 (MQ=255)
                              tCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTg                                              <  1:3275344/66‑1 (MQ=255)
                              tCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTg                                              <  1:3325917/66‑1 (MQ=255)
                              tCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCcgcg                                         <  1:2687496/71‑1 (MQ=255)
                               cATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCcgcg                                         >  1:758999/1‑70 (MQ=255)
                                aTCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTCCCGCGa                                        <  1:3195477/70‑1 (MQ=255)
                                aTCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTCCATTCGCCCGCGa                                        <  1:4404115/70‑1 (MQ=255)
                                aTCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTCCATTCGCCCGCGa                                        <  1:2489930/70‑1 (MQ=255)
                                 tCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCAtt                                                 >  1:2873788/1‑60 (MQ=255)
                                  ccAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTc                                                >  1:2494560/1‑60 (MQ=255)
                                        aCTCCCGCAGTAGCTGTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt                               >  1:931132/1‑71 (MQ=255)
                                        aCTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt                               <  1:3624108/71‑1 (MQ=255)
                                            ccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCa                                                   <  1:3438087/47‑1 (MQ=255)
                                            ccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGt                            <  1:2983139/70‑1 (MQ=255)
                                            ccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTg                           >  1:685074/1‑71 (MQ=255)
                                            ccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTg                           >  1:2846382/1‑71 (MQ=255)
                                            ccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTg                           >  1:1699024/1‑71 (MQ=255)
                                            ccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTg                           >  1:2956170/1‑71 (MQ=255)
                                              gCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGa                                        >  1:1446041/1‑56 (MQ=255)
                                                  tAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTc                                                     <  1:4290717/39‑1 (MQ=255)
                                                  tAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt                               <  1:2335113/61‑1 (MQ=255)
                                                  tAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGc                      <  1:3053385/70‑1 (MQ=255)
                                                   aGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGc                      >  1:3313562/1‑69 (MQ=255)
                                                    gCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCt                                               <  1:792687/43‑1 (MQ=255)
                                                      tctTCGACGTCCGGCGTATCAAACGGCGCAGCTTCAAt                                                  <  1:1875154/38‑1 (MQ=255)
                                                       ctTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGgcg                >  1:2500709/1‑71 (MQ=255)
                                                        ttCGACGTCCGGCGTATCAAACGGCGCAGCTTCCa                                                   >  1:1233171/1‑35 (MQ=255)
                                                        ttCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGgcgc               >  1:4548554/1‑71 (MQ=255)
                                                         tCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCt                                               <  1:4419259/38‑1 (MQ=255)
                                                         tCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTg                           >  1:618770/1‑58 (MQ=255)
                                                          cGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGgcg                <  1:3539393/68‑1 (MQ=255)
                                                          cGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTg             >  1:4329289/1‑71 (MQ=255)
                                                           gACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTg             >  1:3888515/1‑70 (MQ=255)
                                                           gACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTg             >  1:514309/1‑70 (MQ=255)
                                                              gTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGcac          <  1:1495239/70‑1 (MQ=255)
                                                                ccGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAgg       >  1:3530728/1‑71 (MQ=255)
                                                                  ggCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAAt                                      <  1:264219/38‑1 (MQ=255)
                                                                     gTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGgtg     >  1:358450/1‑68 (MQ=255)
                                                                     gTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAg  <  1:2239971/71‑1 (MQ=255)
                                                                      tATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGca           <  1:4601654/61‑1 (MQ=255)
                                                                      tATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGgtg     >  1:3313405/1‑67 (MQ=255)
                                                                      tATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGgtg     >  1:1779240/1‑67 (MQ=255)
                                                                      |                                                                     
CCATTCTCCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTGCACAGGTGTAG  >  minE/1981884‑1982023

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