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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,066,377 G→A 29.6% noncoding (67/76 nt) ileX → tRNA‑Ile

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,066,3770GA29.6% 71.1 / 35.7 54noncoding (67/76 nt)ileXtRNA‑Ile
Reads supporting (aligned to +/- strand):  ref base G (20/18);  new base A (7/9);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 7.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.77e-01

CCATGGCCCCTTAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGCCTTTTTCTTTTTATATA  >  minE/2066307‑2066435
                                                                      |                                                          
ccATGGCCCCTTAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCcagcag                                                            >  1:5123016/1‑71 (MQ=255)
ccATGGCCCCTTAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCcagcag                                                            >  1:2263708/1‑71 (MQ=255)
 cATGGCCCCTTAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAgg                                                           <  1:1355282/71‑1 (MQ=255)
  aaggCCCTTTAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAagg                                                          >  1:4133275/3‑71 (MQ=255)
   tGGCCCCTTAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAggg                                                          >  1:4645995/1‑70 (MQ=255)
         tttAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGccacc                                                    >  1:1036519/2‑70 (MQ=255)
          ttAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGccacca                                                   >  1:1357557/1‑70 (MQ=255)
          ttAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGccacca                                                   >  1:422797/1‑70 (MQ=255)
           tAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGccacca                                                   <  1:572832/69‑1 (MQ=255)
            aGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAg                                                  <  1:1322645/69‑1 (MQ=255)
             gCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGata                                               >  1:3608732/1‑71 (MQ=255)
                  gTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGc                                           >  1:2997517/1‑70 (MQ=255)
                  gTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCa                                          <  1:5442814/71‑1 (MQ=255)
                   tGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCa                                          <  1:4858915/70‑1 (MQ=255)
                    ggTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAgg                                                           >  1:3292934/1‑52 (MQ=255)
                    ggTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAgg                                                           >  1:1942370/1‑52 (MQ=255)
                     gTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCaaa                                        <  1:1784604/70‑1 (MQ=255)
                     gTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCaaa                                        <  1:4865415/70‑1 (MQ=255)
                     gTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAg                                       >  1:3068878/1‑71 (MQ=255)
                         gagCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCt                                    <  1:2454751/70‑1 (MQ=255)
                            cAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGAtata                                             >  1:3358227/1‑58 (MQ=255)
                              ggCTACTCATAATCGCTTGGGCGCTGGTTCAAGTCCAGGAGGGGCCACCAGATAAAGCAAAGGCTGACga                               <  1:351172/70‑1 (MQ=255)
                               gCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGa                                                 <  1:583191/51‑1 (MQ=255)
                                   cTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGccac                                                     <  1:1313762/43‑1 (MQ=255)
                                     cATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGccacca                                                   >  1:1125260/1‑43 (MQ=255)
                                     cATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGCCACCAAat                                                <  1:3372441/46‑1 (MQ=38)
                                     cATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGCCACCAAat                                                <  1:4674033/46‑1 (MQ=38)
                                      aTAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGt                       >  1:3083097/1‑70 (MQ=255)
                                      aTAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGCCACCAAatc                                               <  1:1905981/46‑2 (MQ=38)
                                      aTAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGCCACCAAatc                                               <  1:3647260/46‑2 (MQ=38)
                                      aTAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGCCACCAAatc                                               <  1:928675/46‑2 (MQ=38)
                                      aTAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGCCACCAAat                                                <  1:2931317/45‑1 (MQ=38)
                                      aTAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGCCACCAAat                                                <  1:1787415/45‑1 (MQ=38)
                                       tAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGaaa                           <  1:1485613/65‑1 (MQ=255)
                                       tAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGCCACCAAatca                                              >  1:4948363/1‑44 (MQ=37)
                                       tAATCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGACACCAAatca                                              >  1:1467686/1‑44 (MQ=37)
                                         aTCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGc                   >  1:1375897/1‑71 (MQ=255)
                                         aTCGCTTGGTCGCTGGTTCAAGTCCAGCAAGGGcca                                                      >  1:983717/1‑36 (MQ=255)
                                             cTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGCcttt               >  1:5351952/1‑71 (MQ=255)
                                             cTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGCcttt               >  1:5207641/1‑71 (MQ=255)
                                                ggTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCt                                    <  1:5086855/47‑1 (MQ=255)
                                                 gTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCg                        <  1:5251642/58‑1 (MQ=255)
                                                   cGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAgg                                      >  1:387323/1‑42 (MQ=255)
                                                   cGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAgg                                      >  1:2780096/1‑42 (MQ=255)
                                                   cGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAgg                                      >  1:1676484/1‑42 (MQ=255)
                                                   cGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGaa                            <  1:4726104/52‑1 (MQ=255)
                                                    gCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCt                                    <  1:3801884/43‑1 (MQ=255)
                                                    gCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGATGAGAAATCGTCAGc                   >  1:4477884/1‑60 (MQ=255)
                                                    gCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGc                   >  1:4036223/1‑60 (MQ=255)
                                                      tGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCa                                          >  1:695421/1‑35 (MQ=255)
                                                      tGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGATTTCTCGTCAGc                   >  1:2943128/1‑58 (MQ=25)
                                                      tGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGATTTCTCGTCAGc                   >  1:1805149/1‑58 (MQ=25)
                                                      tGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAAt                          >  1:2579654/1‑51 (MQ=255)
                                                      tGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGCCTTTTTCTTTTta      >  1:2800940/1‑71 (MQ=255)
                                                        gTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGCCTTTTTCTTTTta      <  1:1002097/69‑1 (MQ=255)
                                                         ttCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACgag                              <  1:4517935/44‑1 (MQ=255)
                                                          tCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTc                      >  1:1682848/1‑51 (MQ=255)
                                                          tCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGCCTTTTTCTTTTtatata  >  1:6062/1‑71 (MQ=255)
                                                               tCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACgag                              <  1:3275010/38‑1 (MQ=255)
                                                               tCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACgag                              <  1:5636818/38‑1 (MQ=255)
                                                               tCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGCCTTTTTCTTTTta      <  1:1357507/62‑1 (MQ=255)
                                                                 cagcagGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCa                     >  1:1614580/1‑45 (MQ=255)
                                                                 cagcagGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCa                     >  1:2336216/1‑45 (MQ=255)
                                                                      |                                                          
CCATGGCCCCTTAGCTCAGTGGTTAGAGCAGGCGACTCATAATCGCTTGGTCGCTGGTTCAAGTCCAGCAGGGGCCACCAGATATAGCAAAGGCTGACGAGAAATCGTCAGCCTTTTTCTTTTTATATA  >  minE/2066307‑2066435

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