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 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,971,874 G→A 47.2% G344G (GGC→GGT)  speA ← biosynthetic arginine decarboxylase, PLP‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,971,8740GA47.2% 8.1 / 77.8 91G344G (GGC→GGT) speAbiosynthetic arginine decarboxylase, PLP‑binding
Reads supporting (aligned to +/- strand):  ref base G (34/14);  new base A (2/41);  total (36/55)
Fisher's exact test for biased strand distribution p-value = 1.67e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCACCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGT  >  minE/1971809‑1971932
                                                                 |                                                          
gTCACCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCa                                                         <  1:1427251/69‑1 (MQ=255)
 tCACCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCa                                                         <  1:2918839/68‑1 (MQ=255)
   acagCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:2234186/4‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACCCGCATCGCCAAt                                                       >  1:2003347/1‑68 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:3281380/1‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:2829949/1‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:3224101/1‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:3239238/1‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:1515087/1‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:96170/1‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:741371/1‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:2641252/1‑69 (MQ=255)
   aCCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:377413/1‑69 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATc                                                      >  1:1873272/1‑67 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:1760810/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:2627913/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:2165584/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:2417785/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:798861/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:1760512/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:2491250/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:2500588/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:2819737/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCg                                                     >  1:1452869/1‑68 (MQ=255)
     cGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTGTTCTTCACACGCATCGCCAATc                                                      >  1:2533810/1‑67 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGTAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGAt                                              <  1:1122073/69‑1 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGAt                                              <  1:1051191/69‑1 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGAt                                              <  1:2403925/69‑1 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGAt                                              <  1:2399743/69‑1 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGAt                                              <  1:3001552/69‑1 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGAt                                              <  1:3266813/69‑1 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGAt                                              <  1:738248/69‑1 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGAt                                              <  1:773605/69‑1 (MQ=255)
           aCCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCAAACGCATCGCCAATCGCCCAGAt                                              <  1:3364/69‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:2947501/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:2988097/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:3168578/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:361707/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:2828910/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:275733/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:2720676/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:1075123/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:2128698/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:2542734/68‑1 (MQ=255)
              agATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:1681679/68‑1 (MQ=255)
               gATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:2637126/68‑1 (MQ=255)
               gATTCGGTGATTACCGTCGGATGTGGCAGACCATTTTCTTCACACGCATCACCAATCGCCCAgatgat                                           <  1:982124/68‑1 (MQ=255)
                  tCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAAtgttg                                       >  1:1436253/1‑69 (MQ=255)
                  tCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAAtgtt                                        >  1:3333425/1‑68 (MQ=255)
                          tACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCg                                 >  1:1304559/1‑67 (MQ=255)
                          tACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGt                                >  1:257588/1‑68 (MQ=255)
                          tACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGt                                >  1:1391267/1‑68 (MQ=255)
                          tACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGt                                >  1:190338/1‑68 (MQ=255)
                          tACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGt                                >  1:3109256/1‑68 (MQ=255)
                          tACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTa                               >  1:2424084/1‑69 (MQ=255)
                                       ggCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTAtt                             <  1:3362527/58‑1 (MQ=255)
                                            aCCATTTTCTTCACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGtt             >  1:1743462/1‑69 (MQ=255)
                                            aCCATTTTCTTCACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGtt             >  1:840556/1‑69 (MQ=255)
                                                 tttCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCg        <  1:653378/69‑1 (MQ=255)
                                                 tttCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCg        <  1:338206/69‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCGTTGAGGCCGTAGTTTAc          <  1:3272108/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:14841/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:3380881/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:592336/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:688253/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:1619740/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:1350291/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:799789/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:871705/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:1125042/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:2616220/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:1960460/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:2702946/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:2577680/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:2753399/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:2758550/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:2838465/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:2873702/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:1656996/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:1957408/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:301720/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:3052200/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:3093049/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:3194919/65‑1 (MQ=255)
                                                   tcttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:1744018/65‑1 (MQ=255)
                                                    cttcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:2971062/64‑1 (MQ=255)
                                                      tcACACGCATCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:319876/62‑1 (MQ=255)
                                                       cacaCGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGATCAGt  >  1:2756158/1‑69 (MQ=255)
                                                       cacaCGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGt  >  1:1919032/1‑69 (MQ=255)
                                                       cacaCGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGt  >  1:255302/1‑69 (MQ=255)
                                                              aTCACCAATCGCCCAGATGATGTTGTTGGCGTATTCATTGAGGCCGTAGTTTAc          <  1:1401356/54‑1 (MQ=255)
                                                                 |                                                          
GTCACCGCACGACCCGATTCGGTGATTACCGTCGGATGCGGCAGACCGTTTTCTTCACACGCATCGCCAATCGCCCAGATAATGTTGTTGGCGTATTCATTGAGGCCGTAGTTCACCGAACAGT  >  minE/1971809‑1971932

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