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
A1 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 1,093,686 T→C V130A (GTA→GCA)  ycdT → predicted diguanylate cyclase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,093,6860TC98.9% 309.2 / ‑4.4 89V130A (GTA→GCA) ycdTpredicted diguanylate cyclase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (26/62);  total (26/63)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

CAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTT  >  W3110S.gb/1093622‑1093748
                                                                |                                                              
cAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt                                                          >  1:772457/1‑71 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt                                                          >  1:220878/1‑71 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt                                                          >  1:2396161/1‑71 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt                                                          >  1:3874469/1‑71 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt                                                          >  1:3519539/1‑71 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTTTCATCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt                                                          >  1:2049360/1‑71 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTTTCATCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt                                                          >  1:2054197/1‑71 (MQ=255)
cAAAATGACATTGCAATCTATTATTTGTATCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt                                                          >  1:118617/1‑71 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:3460744/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:2029253/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:2649194/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:2984898/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:3507523/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:3826785/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:3951197/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:395339/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:85878/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:930532/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTATGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:3199781/70‑1 (MQ=255)
       aCATTGCAATCTATTATTTGTTTCGTCAGATGAGTATGTGCATATTAATATTTCTGGCATTGGTGAATaa                                                    <  1:3195008/70‑1 (MQ=255)
               aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:1098411/53‑1 (MQ=255)
               aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:3336244/53‑1 (MQ=255)
               aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:3121177/53‑1 (MQ=255)
               aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:2606571/53‑1 (MQ=255)
               aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:4012733/53‑1 (MQ=255)
               aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:525762/53‑1 (MQ=255)
               aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:1652321/53‑1 (MQ=255)
               aTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:107260/53‑1 (MQ=255)
                  tattatTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATa                                                     <  1:3222175/58‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa                                        <  1:2696330/69‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaa                                          <  1:2332029/67‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:3745635/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:2874876/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:1753544/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:1649145/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:163620/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:3597560/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:2562765/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:2526441/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:16262/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:232670/70‑1 (MQ=255)
                    ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAac                                       <  1:857793/70‑1 (MQ=255)
                       tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAAcaca                                    >  1:516776/1‑70 (MQ=255)
                       tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa                                   <  1:1437720/71‑1 (MQ=255)
                       tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa                                   <  1:6564/71‑1 (MQ=255)
                       tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa                                   <  1:2727121/71‑1 (MQ=255)
                       tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa                                   <  1:1793186/71‑1 (MQ=255)
                       tttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa                                   <  1:2126926/71‑1 (MQ=255)
                        ttGTTTGGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt                                                             <  1:2228044/44‑1 (MQ=38)
                        ttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa                                   <  1:2131645/70‑1 (MQ=255)
                        ttGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaa                                   <  1:2010383/70‑1 (MQ=255)
                                    aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa                                        <  1:1749761/53‑1 (MQ=255)
                                     tGAGTTTGTGCATATTAATATTTCTGGCATTGGTTAATAAAGTTAGTGAAAACACAAAACAGCGCAattta                     >  1:1630639/1‑71 (MQ=255)
                                     tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAg                                              >  1:182681/1‑46 (MQ=255)
                                     tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattta                     <  1:1974669/71‑1 (MQ=255)
                                     tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattta                     <  1:1463438/71‑1 (MQ=255)
                                     tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattta                     <  1:3316254/71‑1 (MQ=255)
                                     tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattta                     <  1:308033/71‑1 (MQ=255)
                                                atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa          <  1:2787213/71‑1 (MQ=255)
                                                atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa          <  1:1262574/71‑1 (MQ=255)
                                                atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa          <  1:1420375/71‑1 (MQ=255)
                                                atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa          <  1:1633505/71‑1 (MQ=255)
                                                atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa          <  1:3055430/71‑1 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAgc                             >  1:3938899/1‑49 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaaaa        >  1:263341/1‑70 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaa             >  1:711658/1‑65 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:628032/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:2293590/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:2814990/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:1588738/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:2923221/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:2811646/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:3653813/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:2741467/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:3373727/1‑71 (MQ=255)
                                                   ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt       >  1:3364571/1‑71 (MQ=255)
                                                     aaTATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa                                        >  1:3295066/1‑36 (MQ=255)
                                                     aaTATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGa     >  1:1821980/1‑71 (MQ=255)
                                                       tatTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACt   <  1:2293732/71‑1 (MQ=255)
                                                       tatTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACt   <  1:2241784/71‑1 (MQ=255)
                                                       tatTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACt   <  1:1352635/71‑1 (MQ=255)
                                                       tatTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACt   <  1:1873501/71‑1 (MQ=255)
                                                         tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATTACtt  <  1:1924752/70‑1 (MQ=255)
                                                         tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACtt  <  1:2549366/70‑1 (MQ=255)
                                                         tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACtt  <  1:55186/70‑1 (MQ=255)
                                                         tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACtt  <  1:620690/70‑1 (MQ=255)
                                                         tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACtt  <  1:1472199/70‑1 (MQ=255)
                                                         tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACtt  <  1:3700833/70‑1 (MQ=255)
                                                         tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATCTTCCAAAAAAATGACtt  <  1:4039922/70‑1 (MQ=255)
                                                                |                                                              
CAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTT  >  W3110S.gb/1093622‑1093748

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