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 2,358,400 G→A 16.4% A362T (GCT→ACT)  glpA → sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,358,4000GA16.4% 205.1 / 27.1 79A362T (GCT→ACT) glpAsn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding
Reads supporting (aligned to +/- strand):  ref base G (23/43);  new base A (8/5);  total (31/48)
Fisher's exact test for biased strand distribution p-value = 1.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCTGAACGCGATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGACTGCCGA  >  W3110S.gb/2358330‑2358464
                                                                      |                                                                
tGCTGAACGCGATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATgg                                                                  >  1:3680735/1‑71 (MQ=255)
 gCTGAACGCGATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGc                                                                 >  1:1875400/1‑71 (MQ=255)
     aaCGCGATGGTCTGGACGTATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGa                                                              <  1:3224863/70‑1 (MQ=255)
      aCGCGATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGaa                                                             >  1:1941297/1‑70 (MQ=255)
      aCGCGATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGACTGAAt                                                            <  1:1509362/71‑1 (MQ=255)
       cgcgATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATg                                                           <  1:2469977/71‑1 (MQ=255)
       cgcgATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATg                                                           <  1:1304229/71‑1 (MQ=255)
       cgcgATGGTCTGGACGGATTTATCACCATCACCGGTGCCAAACTGATGACCTATCGGCTGATGGCTGAATg                                                           <  1:661099/71‑1 (MQ=255)
          gATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGc                                                        <  1:3947141/71‑1 (MQ=255)
           aTGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCt                                                       <  1:2203208/71‑1 (MQ=255)
           aTGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCt                                                       <  1:4445487/71‑1 (MQ=255)
            tGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGaa                                                             >  1:3888568/1‑64 (MQ=255)
            tGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCt                                                       >  1:406337/1‑70 (MQ=255)
              gTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTAcc                                                    <  1:92956/71‑1 (MQ=255)
               tCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCg                                                   <  1:1720895/71‑1 (MQ=255)
               tCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCg                                                   <  1:4432531/71‑1 (MQ=255)
                     cGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCgg                                             <  1:1533954/71‑1 (MQ=255)
                       gATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTa                                           <  1:3539173/71‑1 (MQ=255)
                        aTTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTAt                                          >  1:560484/1‑71 (MQ=255)
                         tttATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATgg                                                                  <  1:3253055/46‑1 (MQ=255)
                         tttATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTa                                           >  1:1659216/1‑69 (MQ=255)
                         tttATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGCCTACCGACGCGGTATg                                         <  1:2897965/71‑1 (MQ=255)
                          ttATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATg                                         <  1:4026034/70‑1 (MQ=255)
                           tATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGc                                        <  1:3961367/70‑1 (MQ=255)
                             tcaccatcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCg                                      <  1:1311726/70‑1 (MQ=255)
                             tcaccatcaccGGTGGCAAACTGATGACCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCg                                      <  1:1623370/70‑1 (MQ=255)
                             tcaccatcaccGGTGGCAAACTGATGACCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCg                                      <  1:1618242/70‑1 (MQ=255)
                              caccatcaccGGTGGCAAACTGATGACCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGc                                     >  1:4318420/1‑70 (MQ=255)
                               accatcaccGGTGGCAAACTTATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCa                                    <  1:2567167/70‑1 (MQ=255)
                               accatcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGc                                        >  1:254534/1‑66 (MQ=255)
                               accatcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCa                                    <  1:3870510/70‑1 (MQ=255)
                               accatcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCa                                    <  1:4009497/70‑1 (MQ=255)
                               accatcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCa                                    <  1:4127626/70‑1 (MQ=255)
                               accatcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCa                                    <  1:3644225/70‑1 (MQ=255)
                               accatcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCa                                    <  1:3625105/70‑1 (MQ=255)
                               accatcaccGGGGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCa                                    <  1:4227446/70‑1 (MQ=255)
                                 catcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAAc                                 <  1:3509871/71‑1 (MQ=255)
                                  atcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCaa                                   <  1:568911/68‑1 (MQ=255)
                                   tcaccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCa                                    <  1:262122/66‑1 (MQ=255)
                                     accGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTgg                              >  1:3048588/1‑70 (MQ=255)
                                      ccGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTgg                              <  1:4183120/69‑1 (MQ=255)
                                        ggTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCaa                          <  1:1950396/71‑1 (MQ=255)
                                        ggTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCaa                          <  1:1983225/71‑1 (MQ=255)
                                         gTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCgg                                             <  1:2928690/51‑1 (MQ=255)
                                         gTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCaa                          >  1:797808/1‑70 (MQ=255)
                                         gTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCaa                          <  1:1720468/70‑1 (MQ=255)
                                         gTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAac                         <  1:368642/71‑1 (MQ=255)
                                         gTGGCAAACTGATGACCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCaa                          >  1:4236379/1‑70 (MQ=255)
                                         gTGGCAAACTGATGACCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCaa                          >  1:3573796/1‑70 (MQ=255)
                                            gCAAACTGATGACCTATCGGCTGATGGCTGAATggg                                                         <  1:1778364/36‑1 (MQ=255)
                                            gCAAACTGATGACCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGCAAACTggg                             >  1:1136124/1‑64 (MQ=255)
                                             cAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACAcgc                     <  1:4207905/71‑1 (MQ=255)
                                               aaCTGATGACCTATCGGCTGATTGCTGAATGGGCTACCGACGCGGTATGc                                        <  1:2515308/50‑1 (MQ=255)
                                               aaCTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACgcgc                   >  1:2825553/1‑71 (MQ=255)
                                                aCTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTa                                           >  1:1839529/1‑46 (MQ=255)
                                                aCTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGcc                  >  1:670550/1‑71 (MQ=255)
                                                aCTGATGACCTATCGGCTGATGGCTGAATGGGCTACAGACGCCGTATGCCGCAAACTGGGCAACACGCGcc                  >  1:2202949/1‑71 (MQ=255)
                                                   gatgaCCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGcccc                >  1:17379/1‑70 (MQ=255)
                                                    atgaCCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTggg                             >  1:194115/1‑56 (MQ=255)
                                                    atgaCCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTg              >  1:504465/1‑71 (MQ=255)
                                                    atgaCCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGCAAAc                                 >  1:915931/1‑52 (MQ=255)
                                                     tgaCCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACAcgc                     >  1:2135588/1‑63 (MQ=255)
                                                     tgaCCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGt             <  1:3513890/71‑1 (MQ=255)
                                                      gaCCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTa            >  1:1627223/1‑71 (MQ=255)
                                                       aCCTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTAc           >  1:1372947/1‑71 (MQ=255)
                                                        ccTATCGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACg          <  1:4251739/71‑1 (MQ=255)
                                                         cTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTg              <  1:3371999/66‑1 (MQ=255)
                                                         cTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGa         >  1:4407990/1‑71 (MQ=255)
                                                         cTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGa         <  1:4455055/71‑1 (MQ=255)
                                                           aTCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGACt       >  1:2614056/1‑71 (MQ=255)
                                                            tCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTTGGCAACACGCGCCCCTGTACGACt       <  1:1445567/70‑1 (MQ=255)
                                                            tCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGAc        <  1:4066775/69‑1 (MQ=255)
                                                            tCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGACt       <  1:4611048/70‑1 (MQ=255)
                                                             cGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAac                         <  1:604713/51‑1 (MQ=255)
                                                             cGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGCaaa                                  >  1:3454110/1‑42 (MQ=255)
                                                             cGGCTGATGACTGAATGGGCTACCGACGCGGTATGCCGCaaa                                  >  1:2040623/1‑42 (MQ=255)
                                                              ggCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGACTGcc    >  1:1678001/1‑71 (MQ=255)
                                                                cTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGACTGCCGa  <  1:1303060/71‑1 (MQ=255)
                                                                 tGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTAc           <  1:4425397/61‑1 (MQ=255)
                                                                   aTGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACt                                >  1:4166496/1‑38 (MQ=255)
                                                                   aTGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACt                                >  1:4160959/1‑38 (MQ=255)
                                                                     ggCTGAATGGGCTACCGACGCGGTATGCCGCAAACt                                >  1:4480957/1‑36 (MQ=255)
                                                                      |                                                                
TGCTGAACGCGATGGTCTGGACGGATTTATCACCATCACCGGTGGCAAACTGATGACCTATCGGCTGATGGCTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGACTGCCGA  >  W3110S.gb/2358330‑2358464

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