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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,015,754 A→G 27.3% C105C (TGT→TGC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,7540AG27.3% 127.8 / 57.1 88C105C (TGT→TGC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (39/25);  new base G (12/12);  total (51/37)
Fisher's exact test for biased strand distribution p-value = 4.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01

ATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAT  >  minE/1015688‑1015824
                                                                  |                                                                      
atcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGa                                                                        >  1:5142457/1‑67 (MQ=255)
atcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGa                                                                        >  1:3467340/1‑67 (MQ=255)
atcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAgg                                                                    <  1:770359/71‑1 (MQ=255)
 tcaCCGCCGCCGGTCCACACGCGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGt                                                                   >  1:4035952/1‑71 (MQ=255)
 tcaCCGCCGCCGGTCCACACGCGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGt                                                                   <  1:243615/71‑1 (MQ=255)
 tcaCCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGa                                                                        <  1:646429/66‑1 (MQ=255)
       ccgccGGTCCACACGCGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAg                                                             <  1:2558444/68‑1 (MQ=255)
       ccaccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAg                                                             <  1:1060718/71‑1 (MQ=255)
        caccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGa                                                            <  1:3155127/71‑1 (MQ=255)
        caccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGa                                                            <  1:304152/71‑1 (MQ=255)
          ccGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGaa                                                           >  1:1963509/1‑70 (MQ=255)
            ggTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGaa                                                           >  1:3296863/1‑68 (MQ=255)
             gTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGcc                                                       >  1:4816617/1‑71 (MQ=255)
             gTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGc                                                        <  1:37240/70‑1 (MQ=255)
               ccATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGa                                                                        >  1:3388531/1‑52 (MQ=255)
                 aTACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAg                                                             <  1:1308118/61‑1 (MQ=255)
                  tACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGc                                                        <  1:3271662/65‑1 (MQ=255)
                   acgcGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTggc                                                 >  1:3611482/4‑71 (MQ=255)
                   acgcGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTggc                                                 >  1:2231729/4‑71 (MQ=255)
                   acgcGCTGGCCGTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTggc                                                 >  1:5263149/4‑71 (MQ=255)
                   acacGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGaa                                                           >  1:3667765/1‑61 (MQ=255)
                    cacGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgcc                                                >  1:5557374/1‑71 (MQ=255)
                     gcGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCtttgg                                                  >  1:3773496/2‑66 (MQ=255)
                      cGCTGGCCTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTggcggc                                              <  1:4973483/71‑1 (MQ=255)
                      cGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:1316713/71‑1 (MQ=255)
                      cGCTGCCCTTTTTAACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:1974887/71‑1 (MQ=255)
                      cGCTGCCCTTTTTAACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:1075037/71‑1 (MQ=255)
                           gccTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTggcggc                                              <  1:4051551/65‑1 (MQ=255)
                            ccTTTTTTACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTc                                        >  1:851234/1‑71 (MQ=255)
                            ccTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTc                                        <  1:2657598/71‑1 (MQ=255)
                             cTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCt                                                      <  1:1546240/56‑1 (MQ=255)
                              ttttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTggcggc                                              <  1:3290668/63‑1 (MQ=255)
                              ttttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTggcggc                                              <  1:4500332/63‑1 (MQ=255)
                              ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:1661459/63‑1 (MQ=255)
                              ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:3174130/63‑1 (MQ=255)
                              ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGa                                            >  1:4324635/1‑65 (MQ=255)
                              ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                       >  1:150716/1‑70 (MQ=255)
                              ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                       >  1:2546137/1‑70 (MQ=255)
                              ttttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                       >  1:1028860/1‑70 (MQ=255)
                               tttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTggcggc                                              <  1:3672295/62‑1 (MQ=255)
                               tttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCg                                       >  1:657737/1‑69 (MQ=255)
                               tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCttt                                                    >  1:5230059/1‑56 (MQ=255)
                               tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCttt                                                    >  1:5193701/1‑56 (MQ=255)
                               tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCttt                                                    >  1:5224497/1‑56 (MQ=255)
                               tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                       >  1:4065337/1‑69 (MQ=255)
                               tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                       >  1:2910695/1‑69 (MQ=255)
                               tttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCg                                       >  1:4703573/1‑69 (MQ=255)
                                ttttACCGACGATGATCGCGGTGCCGGTATCCTGGCa                                                                      >  1:3142188/1‑37 (MQ=21)
                                ttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGt                                                                   >  1:4556733/1‑40 (MQ=25)
                                ttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGt                                                                   >  1:1528893/1‑40 (MQ=25)
                                ttttACCGACGATGATCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAg                                    >  1:5225673/1‑71 (MQ=255)
                                ttttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGc                                                               >  1:1806926/1‑44 (MQ=255)
                                 tttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGt                                   >  1:1643407/1‑71 (MQ=255)
                                  ttACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGt                                   <  1:2777173/70‑1 (MQ=255)
                                    aCCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGa                                            >  1:5517858/1‑59 (MQ=255)
                                    aCCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGa                                            >  1:3033088/1‑59 (MQ=255)
                                        acaaTAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:5196834/53‑1 (MQ=255)
                                        acaaTAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:2455454/53‑1 (MQ=255)
                                        acaaTAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:5245579/53‑1 (MQ=255)
                                        acaaTAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTcgccgc                                              <  1:1375116/53‑1 (MQ=255)
                                         caaTAATCGCGGTGCCGGTATCCTGACAGGTTGGCAg                                                             <  1:4250178/37‑1 (MQ=255)
                                         caaTAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAgg                           <  1:1928952/71‑1 (MQ=255)
                                          aataatCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGa                                            >  1:3682989/1‑53 (MQ=255)
                                          aataatCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGa                                            >  1:3880397/1‑53 (MQ=255)
                                          aataatCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGa                                            >  1:3872794/1‑53 (MQ=255)
                                          aataatCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAgg                           >  1:3286898/1‑70 (MQ=255)
                                           ataatCGCGGTGCCGGTATCCTGACAGGTTGGCAGaa                                                           >  1:3048017/1‑37 (MQ=255)
                                           ataatCGCGGTGCCGGTATCCTGACAGGTTGGCAGaa                                                           >  1:3298993/1‑37 (MQ=255)
                                            taatCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAAt                        >  1:2007616/1‑71 (MQ=255)
                                              atCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTg                      <  1:3132523/71‑1 (MQ=255)
                                              atCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTg                      <  1:791435/71‑1 (MQ=255)
                                               tCGCGGTGCCGGTATCCTGGCAGGTCGGCAGCACGcc                                                       <  1:2539707/37‑1 (MQ=25)
                                                      gCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCca              >  1:4192488/1‑71 (MQ=255)
                                                       ccGGTATCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCcac             >  1:998317/1‑71 (MQ=255)
                                                       ccGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGa                                            >  1:346272/1‑40 (MQ=255)
                                                         ggTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCcac             >  1:1102281/1‑69 (MQ=255)
                                                           tATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACata          <  1:3301211/70‑1 (MQ=255)
                                                            aTCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt        >  1:5109385/1‑71 (MQ=255)
                                                            aTCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt        >  1:3329695/1‑71 (MQ=255)
                                                             tCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCcacg            <  1:5676077/66‑2 (MQ=255)
                                                             tCCTGGCAGGTCGGCAGCACGCCTTTGGCGGCGATTTCGGAGTTTCTTAAGAATTGCAGCGCCACgtac         <  1:4853166/69‑2 (MQ=255)
                                                             tCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGc                     <  1:1596908/57‑1 (MQ=255)
                                                             tCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCca              <  1:1046048/64‑1 (MQ=255)
                                                             tCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt        >  1:4150612/1‑70 (MQ=255)
                                                             tCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATAtt        >  1:542707/1‑70 (MQ=255)
                                                               cTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTa      <  1:3355582/70‑1 (MQ=255)
                                                               cTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTAt     >  1:3885883/1‑71 (MQ=255)
                                                               cTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTAt     >  1:1937606/1‑71 (MQ=255)
                                                                 gACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTg                      >  1:3165474/1‑52 (MQ=255)
                                                                 gACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCa                    >  1:4388660/1‑54 (MQ=255)
                                                                 gACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCa                    >  1:4178052/1‑54 (MQ=255)
                                                                 gACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCa                    >  1:2935923/1‑54 (MQ=255)
                                                                  aCAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATc    <  1:1445599/69‑1 (MQ=255)
                                                                  aCAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAt  >  1:4058642/1‑71 (MQ=255)
                                                                  aCAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAt  >  1:1035501/1‑71 (MQ=255)
                                                                  |                                                                      
ATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCGCGGTGCCGGTATCCTGACAGGTTGGCAGAACGCCTTTCGCCGCGATGTCGGAGTTACGCAGGAATTGCAGCGCCACATATTTATCAT  >  minE/1015688‑1015824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A