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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 702,273 C→T 14.6% D301N (GAT→AAT)  nagA ← N‑acetylglucosamine‑6‑phosphate deacetylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb702,2730CT14.6% 220.8 / 25.5 82D301N (GAT→AAT) nagAN‑acetylglucosamine‑6‑phosphate deacetylase
Reads supporting (aligned to +/- strand):  ref base C (32/38);  new base T (4/8);  total (36/46)
Fisher's exact test for biased strand distribution p-value = 5.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.58e-01

CAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCACCTGC  >  W3110S.gb/702203‑702342
                                                                      |                                                                     
cAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc                                                                       >  1:3771806/1‑71 (MQ=255)
cAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc                                                                       >  1:1897041/1‑71 (MQ=255)
cAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc                                                                       >  1:851715/1‑71 (MQ=255)
 aaTGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCAAcc                                                                      <  1:4128288/71‑1 (MQ=255)
   tGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCcac                                                                    <  1:1014393/71‑1 (MQ=255)
       cGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTcacaca                                                                 <  1:2041573/70‑1 (MQ=255)
       cGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCcacaca                                                                 >  1:3442048/1‑70 (MQ=255)
        gACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACaaa                                                               <  1:2896943/71‑1 (MQ=255)
        gACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACaa                                                                <  1:1599693/70‑1 (MQ=255)
        gACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACaa                                                                <  1:2982613/70‑1 (MQ=255)
         aCCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAg                                                              <  1:1106396/71‑1 (MQ=255)
         aCCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAg                                                              >  1:808162/1‑71 (MQ=255)
          ccAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc                                                                       >  1:3964574/1‑61 (MQ=255)
          ccAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc                                                                       >  1:3610487/1‑61 (MQ=255)
           cAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTc                                                            >  1:2962538/1‑71 (MQ=255)
           cAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTc                                                            >  1:2134104/1‑71 (MQ=255)
            aGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTcc                                                           <  1:1711164/71‑1 (MQ=255)
            aGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTcc                                                           <  1:3139198/71‑1 (MQ=255)
             gATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATc                                                                       <  1:587848/58‑1 (MQ=255)
             gATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCg                                                          >  1:1217132/1‑71 (MQ=255)
                 acgcacgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTa                                                       <  1:4427572/70‑1 (MQ=255)
                      cgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtag                                                 <  1:4191800/71‑1 (MQ=255)
                      cgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtag                                                 >  1:508452/1‑71 (MQ=255)
                      cgcCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtag                                                 <  1:4396341/71‑1 (MQ=255)
                          ttCAATCATGGTTAAGGATGCACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGtata                                             >  1:513618/1‑71 (MQ=255)
                          ttCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGt                                                         <  1:2835763/59‑1 (MQ=255)
                           tCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTAc                                                      <  1:2769297/61‑1 (MQ=255)
                           tCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgta                                                  >  1:3793706/1‑65 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGtata                                             <  1:2136866/69‑1 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTatat                                            >  1:873120/1‑70 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTatat                                            >  1:3757602/1‑70 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATAtt                                           >  1:3534682/1‑71 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTa                                                       >  1:1243129/1‑59 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTa                                                       >  1:715192/1‑59 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTatat                                            <  1:1318070/70‑1 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTatat                                            >  1:2863980/1‑70 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTatat                                            <  1:3516507/70‑1 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATAtt                                           >  1:3345608/1‑71 (MQ=255)
                            cAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATAtt                                           >  1:3510797/1‑71 (MQ=255)
                             aaTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGtata                                             <  1:1288199/68‑1 (MQ=255)
                             aaTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATAtt                                           <  1:4022566/70‑1 (MQ=255)
                             aaTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg                                          <  1:3027058/71‑1 (MQ=255)
                             aaTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg                                          >  1:447584/1‑71 (MQ=255)
                             aaTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg                                          <  1:457311/71‑1 (MQ=255)
                             aaTCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg                                          <  1:2115765/71‑1 (MQ=255)
                               tCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACaa                                                                <  1:2700942/47‑1 (MQ=255)
                               tCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAg                                                              <  1:881280/49‑1 (MQ=255)
                               tCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtt                                        <  1:4101109/71‑1 (MQ=255)
                                cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACaaa                                                               >  1:1685142/1‑47 (MQ=255)
                                cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCg                                                          >  1:213624/1‑52 (MQ=255)
                                cATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGttt                                       >  1:871229/1‑71 (MQ=255)
                                 aTGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGttt                                       >  1:1095591/1‑70 (MQ=255)
                                   ggTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtagta                                               <  1:3690028/60‑1 (MQ=255)
                                     ttAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgta                                                  <  1:4385624/55‑1 (MQ=255)
                                     ttAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTAccc                                  >  1:3455401/1‑71 (MQ=255)
                                         ggATGAACCGCTTAGCGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCa                               >  1:4427472/1‑70 (MQ=255)
                                         ggATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgta                                                  <  1:628847/51‑1 (MQ=255)
                                         ggATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCa                               >  1:1742018/1‑70 (MQ=255)
                                          gATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgta                                                  <  1:1079987/50‑1 (MQ=255)
                                           aTGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACgg                                                    >  1:2784310/1‑47 (MQ=255)
                                           aTGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaa                             >  1:4361737/1‑70 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATAtt                                           >  1:95402/1‑53 (MQ=255)
                                              aaCCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATg                         <  1:413541/71‑1 (MQ=255)
                                               aCCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGa                        <  1:2887237/71‑1 (MQ=255)
                                                ccGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGgtagta                                               <  1:2714654/47‑1 (MQ=255)
                                                ccGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTg                                          >  1:1779648/1‑52 (MQ=255)
                                                ccGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGaa                       <  1:3427549/71‑1 (MQ=255)
                                                 cGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTa                                     >  1:1969202/1‑56 (MQ=255)
                                                  gCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACt                     <  1:2133658/71‑1 (MQ=255)
                                                   cTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTAc                                    <  1:696970/55‑1 (MQ=255)
                                                   cTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTg                    <  1:2540826/71‑1 (MQ=255)
                                                     tAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGtt                  >  1:97242/1‑71 (MQ=255)
                                                      aaCGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGt                   <  1:3766715/69‑1 (MQ=255)
                                                      aaCGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGtttt                                      <  1:2137489/50‑1 (MQ=255)
                                                      aaCGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGt                   <  1:2490052/69‑1 (MQ=255)
                                                        cGTACCGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCaa               >  1:4470578/1‑71 (MQ=255)
                                                          tACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATg             <  1:3613012/71‑1 (MQ=255)
                                                            ccGTTCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGt            <  1:2534027/70‑1 (MQ=255)
                                                            ccGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGtt           >  1:3705239/1‑71 (MQ=255)
                                                            ccGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGt            <  1:1803912/70‑1 (MQ=255)
                                                            ccGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGt            <  1:2581373/70‑1 (MQ=255)
                                                               ttCTCATTCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCa                <  1:1908090/63‑1 (MQ=255)
                                                                 ctcATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGCACTGTTCAATGTTGGCAc      >  1:218410/1‑71 (MQ=255)
                                                                  tcATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGt            <  1:1882767/64‑1 (MQ=255)
                                                                    aTCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCaaa                             <  1:2629557/45‑1 (MQ=255)
                                                                    aTCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCAc      >  1:4616404/1‑68 (MQ=255)
                                                                    aTCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCACctg   >  1:919799/1‑71 (MQ=255)
                                                                    aTCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCACct    <  1:2106205/70‑1 (MQ=255)
                                                                     tCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCACctgc  >  1:1875206/1‑71 (MQ=255)
                                                                      |                                                                     
CAATGTTCGACCAGATTACGCACGCCTTCAATCATGGTTAAGGATGAACCGCTTAACGTACCGTTCTCATCCACACAAAGTCCGTTACGGTAGTATATTGTTTTACCCGCAAAAATGAACTGTTCAATGTTGGCACCTGC  >  W3110S.gb/702203‑702342

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