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 2,405,535 A→G 37.7% Y642Y (TAT→TAC)  cyaA ← adenylate cyclase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,405,5350AG37.7% 25.3 / 32.2 53Y642Y (TAT→TAC) cyaAadenylate cyclase
Reads supporting (aligned to +/- strand):  ref base A (18/15);  new base G (8/12);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 3.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

TCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCAT  >  minE/2405473‑2405582
                                                              |                                               
tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                           <  1:708463/69‑1 (MQ=255)
tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                           <  1:2846674/69‑1 (MQ=255)
tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                           <  1:3335254/69‑1 (MQ=255)
tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                           <  1:1538852/69‑1 (MQ=255)
tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                           <  1:1422025/69‑1 (MQ=255)
tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                           <  1:1391511/69‑1 (MQ=255)
tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                           <  1:355186/69‑1 (MQ=255)
tCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACag                                           <  1:1111591/69‑1 (MQ=255)
   aTACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACagaa                                         <  1:1323698/68‑1 (MQ=255)
   aTACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACagaa                                         <  1:3431183/68‑1 (MQ=255)
   aTACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACagaa                                         <  1:2775273/68‑1 (MQ=255)
   aTACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACagaa                                         <  1:3290710/68‑1 (MQ=255)
      cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGAc                                      >  1:2162810/1‑68 (MQ=255)
      cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                                     >  1:2413519/1‑69 (MQ=255)
      cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                                     >  1:378332/1‑69 (MQ=255)
      cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                                     >  1:2457303/1‑69 (MQ=255)
      cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                                     >  1:173397/1‑69 (MQ=255)
      cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                                     >  1:1074664/1‑69 (MQ=255)
      cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                                     >  1:1578578/1‑69 (MQ=255)
      cacTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACt                                     >  1:436693/1‑69 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:3074198/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:296929/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:825665/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:546030/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:471675/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:223546/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:1110951/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:210619/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:1716287/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:1680263/68‑1 (MQ=255)
             aaaCCAGTTGCTGCACGCGAGTACGGATTAAGCCGAGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:2767666/68‑1 (MQ=255)
               aCCAGTTGCTGCACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACg                               <  1:670601/66‑1 (MQ=255)
               aCCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTa                            <  1:3240112/69‑1 (MQ=255)
                   gTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTg                        >  1:533604/1‑69 (MQ=255)
                   gTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTg                        >  1:522111/1‑69 (MQ=255)
                      gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg                     >  1:3435593/1‑69 (MQ=255)
                      gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg                     >  1:467959/1‑69 (MQ=255)
                      gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg                     >  1:1122169/1‑69 (MQ=255)
                      gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg                     >  1:1205545/1‑69 (MQ=255)
                      gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg                     >  1:364318/1‑69 (MQ=255)
                      gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg                     >  1:3345405/1‑69 (MQ=255)
                      gctgcACGCGAGTACGGATTAAGCCGCGCAGATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCg                     >  1:2719789/1‑69 (MQ=255)
                      gctgcACGCGAGTACGGATTAAGCCGCG‑‑GATGCTGGCTGTAGCAGAAGACTTCCACGCTATCTGGCGGt                   >  1:1119027/1‑69 (MQ=255)
                      gctgcACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCg                     >  1:1559663/1‑69 (MQ=255)
                      gctgcACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCg                     >  1:1585904/1‑69 (MQ=255)
                      gctgcACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCg                     >  1:1801266/1‑69 (MQ=255)
                      gctgcACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCg                     >  1:2662520/1‑69 (MQ=255)
                                  tACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCt         <  1:1291375/69‑1 (MQ=255)
                                  tACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCt         <  1:1056814/69‑1 (MQ=255)
                                   aCGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTg        >  1:2072314/1‑69 (MQ=255)
                                         tAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTgcggcg             >  1:511682/1‑58 (MQ=255)
                                         tAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCAt  >  1:2311895/1‑69 (MQ=255)
                                         tAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCAt  >  1:101633/1‑69 (MQ=255)
                                                              |                                               
TCAATACACTCAGAAACCAGTTGCTGCACGCGAGTACGAATTAAGCCGCGCAGATGCTGGCTATAACAGAAGACTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCAT  >  minE/2405473‑2405582

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