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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,449,567 C→T 23.1% V17I (GTT→ATT)  yfcL ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,449,5670CT23.1% 156.7 / 44.5 78V17I (GTT→ATT) yfcLhypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/37);  new base T (9/9);  total (32/46)
Fisher's exact test for biased strand distribution p-value = 4.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.02e-01

ATGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTAA  >  W3110S.gb/2449500‑2449633
                                                                   |                                                                  
aTGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCAt                                                                 <  1:2104569/71‑1 (MQ=255)
aTGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCAt                                                                 <  1:2441643/71‑1 (MQ=255)
        tGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATAcc                                                              <  1:2400392/66‑1 (MQ=255)
        tGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATAcc                                                              <  1:3449853/66‑1 (MQ=255)
        tGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATAcc                                                              <  1:1463220/66‑1 (MQ=255)
        tGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTc                                                           <  1:3874017/69‑1 (MQ=255)
         gTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAt                                                        >  1:1156047/1‑71 (MQ=255)
         gTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAt                                                        >  1:3473154/1‑71 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACACCTCATCATCACTGGCATGGTCAATCATACCg                                                             >  1:3562241/1‑65 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGAtt                                                       <  1:3632846/71‑1 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGAt                                                        >  1:757967/1‑70 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGAt                                                        >  1:1292720/1‑70 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGt                                                            >  1:3199190/1‑66 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGt                                                            >  1:2003928/1‑66 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGt                                                            >  1:2186184/1‑66 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:3182315/71‑1 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:2259875/71‑1 (MQ=255)
                  ccACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                               <  1:54153/71‑1 (MQ=255)
                   cACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                               <  1:1967946/70‑1 (MQ=255)
                       cAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGa                                                         >  1:2644297/1‑56 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGt                                        >  1:3314947/1‑71 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:536118/56‑1 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:327214/56‑1 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:598190/56‑1 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:952509/56‑1 (MQ=255)
                         aaTACCCACTGGCAAACAACTAATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:1454330/56‑1 (MQ=255)
                               cACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                  <  1:2975251/71‑1 (MQ=255)
                               cACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTc                                   >  1:772818/1‑70 (MQ=255)
                               cACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                  <  1:3422957/71‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAg                                               <  1:1977765/56‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAg                                               <  1:631052/56‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCAt                                                                 <  1:373707/38‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCAt                                                                 <  1:1631646/38‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                               <  1:3534083/56‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                               <  1:3406368/56‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                               <  1:1358003/56‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                               <  1:3238229/56‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                               <  1:375469/56‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCaaa                                <  1:2266862/71‑1 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                  <  1:873226/69‑1 (MQ=255)
                                   ggCAAACAACTCATCATCACTGGCATGGTCAACCATAc                                                               >  1:688835/1‑38 (MQ=255)
                                   ggCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCg                                         >  1:3836358/1‑60 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAACCATAcc                                                              >  1:3525117/1‑38 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAACCATAcc                                                              >  1:3080784/1‑38 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAACCATAcc                                                              >  1:1566287/1‑38 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAACCATAcc                                                              >  1:1373018/1‑38 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAACCATAcc                                                              >  1:3878082/1‑38 (MQ=255)
                                       aacaacTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:48744/42‑1 (MQ=255)
                                       aacaacTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:1212272/42‑1 (MQ=255)
                                       aacaacTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:2577812/42‑1 (MQ=255)
                                       aacaacTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:3050013/42‑1 (MQ=255)
                                        acaacTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                       <  1:2458625/41‑1 (MQ=255)
                                         caacTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAGaa                                             >  1:3795882/1‑50 (MQ=255)
                                         caacTCATCATCACTGGCATGGTCAACCATACCGTCGATTaa                                                     >  1:3879846/1‑42 (MQ=255)
                                         aaacTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCa                                                >  1:3111982/2‑47 (MQ=255)
                                           acTCATCATCACTGGCATGGT‑AACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGatca                     <  1:2966105/71‑1 (MQ=255)
                                            cTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGatca                     <  1:3341098/71‑1 (MQ=255)
                                              catcatcaCTGGCATGGTCAACCATACCGTCGATTAATGACAGaa                                             >  1:907842/1‑45 (MQ=255)
                                                tcatcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCAtctt                 <  1:2809301/71‑1 (MQ=255)
                                                  atcaCTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCAtcttct               >  1:2212705/1‑71 (MQ=255)
                                                  atcaCTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGAATCAAACTCCGCGATCAtcttct               >  1:2581990/1‑71 (MQ=255)
                                                   tcaCTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCg                                         <  1:3363974/44‑1 (MQ=255)
                                                   tcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                  <  1:155474/51‑1 (MQ=255)
                                                   tcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATcttctt              <  1:3875841/71‑1 (MQ=255)
                                                    caCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGatca                     >  1:2407288/1‑63 (MQ=255)
                                                    caCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGatca                     >  1:2619885/1‑63 (MQ=255)
                                                     aCTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTg                                       >  1:136783/1‑44 (MQ=255)
                                                     aCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTc            >  1:2848910/1‑71 (MQ=255)
                                                     aCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTc            >  1:948837/1‑71 (MQ=255)
                                                         gCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTc         <  1:1847349/70‑1 (MQ=255)
                                                         gCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTc         <  1:1598831/70‑1 (MQ=255)
                                                         gCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTc         <  1:2753917/70‑1 (MQ=255)
                                                         gCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTc         <  1:3634420/70‑1 (MQ=255)
                                                         gCATGGT‑AACCATACCGTCGATTAATGCCAGAATGCg                                         >  1:1659075/1‑37 (MQ=38)
                                                              gTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGt    >  1:2310732/1‑70 (MQ=255)
                                                              gTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGt    >  1:1681920/1‑70 (MQ=255)
                                                              gTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTa   <  1:3296275/71‑1 (MQ=255)
                                                               tCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTaa  <  1:1864855/71‑1 (MQ=255)
                                                                   ccATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCttt             <  1:3497755/56‑1 (MQ=255)
                                                                   ccATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCttt             <  1:3576391/56‑1 (MQ=255)
                                                                   |                                                                  
ATGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTAA  >  W3110S.gb/2449500‑2449633

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A