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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 498,441 C→T 44.2% G24S (GGT→AGT)  galE ← UDP‑galactose‑4‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE498,4410CT44.2% 74.7 / 221.8 165G24S (GGT→AGT) galEUDP‑galactose‑4‑epimerase
Reads supporting (aligned to +/- strand):  ref base C (55/37);  new base T (39/34);  total (94/71)
Fisher's exact test for biased strand distribution p-value = 4.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-01

Only 100 of 165 total aligned reads displayed.

AACGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCA  >  minE/498372‑498509
                                                                     |                                                                    
aaCGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCg                                                                     >  1:2160358/1‑71 (MQ=255)
aaCGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCg                                                                     >  1:2577727/1‑71 (MQ=255)
  cGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtt                                                                   >  1:126373/1‑71 (MQ=255)
  cGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtt                                                                   >  1:2088244/1‑71 (MQ=255)
  cGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtt                                                                   >  1:3536634/1‑71 (MQ=255)
  cGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtt                                                                   >  1:1429114/1‑71 (MQ=255)
  cGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtt                                                                   >  1:175166/1‑71 (MQ=255)
       gATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGtttt                                                                 >  1:1645550/1‑68 (MQ=255)
       gATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTg                                                                <  1:3995892/69‑1 (MQ=255)
         tAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                            <  1:2112318/71‑1 (MQ=255)
         tAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                            <  1:1291462/71‑1 (MQ=255)
              ggCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTg                                                       <  1:2292429/71‑1 (MQ=255)
              ggCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTg                                                       <  1:2633337/71‑1 (MQ=255)
                cAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGca                                                     <  1:633857/71‑1 (MQ=255)
                   tACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGc                                                               <  1:1596124/58‑1 (MQ=255)
                   tACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGc                                                               <  1:2251060/58‑1 (MQ=255)
                   tACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGc                                                               <  1:890884/58‑1 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGcacaca                                                 <  1:2405054/70‑1 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAg                                                >  1:3721998/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAg                                                >  1:417390/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAg                                                >  1:3434153/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTCTTTTGCAGTAATTGcacaca                                                 >  1:4089371/1‑70 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAg                                                             >  1:355464/1‑58 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:3345689/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:3822364/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:2781695/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:2273852/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:3464470/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:3165846/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:4122374/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:924377/1‑71 (MQ=255)
                       cTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAgg                                               >  1:61689/1‑70 (MQ=255)
                       cTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAgg                                               >  1:3868221/1‑70 (MQ=255)
                        tGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:1932635/1‑68 (MQ=255)
                        tGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:1774318/1‑68 (MQ=255)
                        tGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                >  1:3575131/1‑68 (MQ=255)
                          cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCATTAATTGCACACAGGTAt                                            <  1:3903595/70‑1 (MQ=255)
                          cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTag                                            <  1:3694701/70‑2 (MQ=255)
                          cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTAt                                            <  1:2066966/70‑1 (MQ=255)
                          cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTCCACACAGGTAt                                            <  1:2730034/70‑1 (MQ=255)
                             ttACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACt                                        >  1:3649735/1‑71 (MQ=255)
                              tACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                            <  1:349986/50‑1 (MQ=255)
                              tACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                            <  1:2902507/50‑1 (MQ=255)
                              tACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTaa                                                          >  1:1402023/1‑52 (MQ=255)
                              tACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACtt                                       >  1:1357231/1‑71 (MQ=255)
                                   ttACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAAt                                                         >  1:1383546/1‑48 (MQ=255)
                                   ttACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCa                                    <  1:135127/69‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                               <  1:3613899/49‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                               <  1:1420250/49‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                               <  1:3390177/49‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                               <  1:1087656/49‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGt                                              <  1:1561475/50‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGt                                              <  1:2579780/50‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGt                                              <  1:1978954/50‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCt                         <  1:270508/71‑1 (MQ=255)
                                             tATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTa                        >  1:216991/1‑71 (MQ=255)
                                             tATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTa                        >  1:3011637/1‑71 (MQ=255)
                                               tCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAgg                                               <  1:3912066/46‑1 (MQ=255)
                                               tCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAgg                                               <  1:53468/46‑1 (MQ=255)
                                               tCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAgg                                               <  1:104065/46‑1 (MQ=255)
                                               tCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAgg                                               <  1:3310179/46‑1 (MQ=255)
                                                cAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:1033957/1‑50 (MQ=255)
                                                cAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:2562978/1‑50 (MQ=255)
                                                cAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:4060922/1‑50 (MQ=255)
                                                cAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:480962/1‑50 (MQ=255)
                                                cAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:896736/1‑50 (MQ=255)
                                                cAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTacca                     >  1:2719310/1‑71 (MQ=255)
                                                 aaGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTaccac                    >  1:2382722/1‑71 (MQ=255)
                                                 aaGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTacaac                    >  1:698838/1‑71 (MQ=255)
                                                   gAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTAt                                            <  1:478365/45‑1 (MQ=255)
                                                   gAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTAt                                            <  1:4122702/45‑1 (MQ=255)
                                                   gAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTAt                                            <  1:2819689/45‑1 (MQ=255)
                                                   gAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTAt                                            <  1:2688626/45‑1 (MQ=255)
                                                   gAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTAt                                            <  1:248899/45‑1 (MQ=255)
                                                   gAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCg                  >  1:2270549/1‑71 (MQ=255)
                                                     atgatgACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:108765/1‑45 (MQ=255)
                                                     atgatgACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:40599/1‑45 (MQ=255)
                                                     atgatgACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:3974016/1‑45 (MQ=255)
                                                     atgatgACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:3809451/1‑45 (MQ=255)
                                                     atgatgACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                          >  1:2684505/1‑45 (MQ=255)
                                                     atgatgACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:1903798/1‑64 (MQ=255)
                                                     atgatgACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:1991399/1‑64 (MQ=255)
                                                      tgatgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGt                >  1:3502698/1‑70 (MQ=255)
                                                       gatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:2999695/1‑62 (MQ=255)
                                                       gatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:3256588/1‑62 (MQ=255)
                                                       gatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:607262/1‑62 (MQ=255)
                                                       gatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:2209930/1‑62 (MQ=255)
                                                       gatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:2227845/1‑62 (MQ=255)
                                                       gatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:2796695/1‑62 (MQ=255)
                                                       gatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       >  1:3745841/1‑62 (MQ=255)
                                                       gatgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTaa              >  1:2885873/1‑71 (MQ=255)
                                                       gatgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTaa              >  1:2349935/1‑71 (MQ=255)
                                                       gatgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTaa              >  1:114707/1‑71 (MQ=255)
                                                        atgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc             <  1:2645054/71‑1 (MQ=255)
                                                           aCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc             >  1:668353/1‑68 (MQ=255)
                                                           aCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAg          <  1:3053754/71‑1 (MQ=255)
                                                            catcatGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAg          <  1:3388272/70‑1 (MQ=255)
                                                              tcatGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTa                               <  1:803793/47‑1 (MQ=255)
                                                              tcatGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTa                               <  1:3244146/47‑1 (MQ=255)
                                                              tcatGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                       <  1:2908182/55‑1 (MQ=255)
                                                                     |                                                                    
AACGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCA  >  minE/498372‑498509

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A