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 2,224,918 C→T 42.7% I189I (ATC→ATT)  prmA → methylase for 50S ribosomal subunit protein L11

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,224,9180CT42.7% 35.0 / 77.7 103I189I (ATC→ATT) prmAmethylase for 50S ribosomal subunit protein L11
Reads supporting (aligned to +/- strand):  ref base C (35/24);  new base T (18/26);  total (53/50)
Fisher's exact test for biased strand distribution p-value = 7.53e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

Only 100 of 103 total aligned reads displayed.

GTTCCGGCATTCTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGAA  >  minE/2224854‑2224984
                                                                |                                                                  
gTTCCGGCATTCTGGCGATCGCGGCGCTGAAACTTGGTGCAGCAAAAGCCATTGGTATTGATATCGATc                                                                <  1:1053640/69‑1 (MQ=255)
gTTCCGGCATTCTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGa                                                                  <  1:2093219/67‑1 (MQ=255)
gTTCCGGCATTCTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATc                                                                <  1:54801/69‑1 (MQ=255)
gTTCCGGCATTCTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATc                                                                <  1:1590323/69‑1 (MQ=255)
gTTCCGGCATTCTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATc                                                                <  1:124739/69‑1 (MQ=255)
           cTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGa                                                       >  1:1234776/1‑67 (MQ=255)
           cTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGa                                                       >  1:7126/1‑67 (MQ=255)
           cTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGa                                                       >  1:3208424/1‑67 (MQ=255)
           cTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGa                                                       >  1:2525692/1‑67 (MQ=255)
           cTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGa                                                       >  1:2537379/1‑67 (MQ=255)
           cTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGa                                                       >  1:2120610/1‑67 (MQ=255)
           cTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGa                                                       >  1:1148987/1‑67 (MQ=255)
           cTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGa                                                       >  1:1033082/1‑67 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2282295/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2366572/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:1874773/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:408008/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2351692/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:1440407/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:205372/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2179010/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:3231976/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2416511/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:567257/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2439/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2447789/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:3052580/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2714528/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:825480/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2817314/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:2912201/60‑1 (MQ=255)
                 aTCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATTGATCCGCAGGCg                                                        <  1:925291/60‑1 (MQ=255)
                           tGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGCCCAGCCGCGAt                                      <  1:2940307/68‑1 (MQ=255)
                            gAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      <  1:807084/67‑1 (MQ=255)
                            gAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      <  1:3215457/67‑1 (MQ=255)
                            gAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      <  1:3059381/67‑1 (MQ=255)
                            gAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      <  1:1369559/67‑1 (MQ=255)
                            gAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      <  1:1404458/67‑1 (MQ=255)
                            gAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATaa                                    <  1:1284749/69‑1 (MQ=255)
                            gAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATaa                                    <  1:1962306/69‑1 (MQ=255)
                            gAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATaa                                    <  1:791071/69‑1 (MQ=255)
                             aaaCTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATaa                                    <  1:2741754/68‑1 (MQ=255)
                                 tGGGTGCAGCAAAAGCCATTGGTATTGATATCGATcc                                                               >  1:2950565/1‑37 (MQ=255)
                                 tGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGAt                                                      >  1:3023270/1‑46 (MQ=255)
                                 tGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCg                               >  1:705883/1‑69 (MQ=255)
                                 tGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCg                               >  1:2772431/1‑69 (MQ=255)
                                 tGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCg                               >  1:3157534/1‑69 (MQ=255)
                                 tGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCg                               >  1:2322007/1‑69 (MQ=255)
                                 tGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCg                               >  1:1203342/1‑69 (MQ=255)
                                     tGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGaa                             <  1:592433/67‑1 (MQ=255)
                                     tGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGaa                             <  1:2572042/67‑1 (MQ=255)
                                      gcagcaAAAGCCATTGTTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGt                          <  1:3259328/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGt                          <  1:1006006/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGt                          <  1:2718619/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGt                          <  1:3096298/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGt                          <  1:3404743/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGt                          <  1:2139701/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGt                          <  1:564507/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGt                          <  1:3312036/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGt                          <  1:887969/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGt                          <  1:2654362/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGt                          <  1:1217643/69‑1 (MQ=255)
                                      gcagcaAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGt                          <  1:2515695/69‑1 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCa                                                   >  1:1742983/1‑42 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAAc                                   >  1:360222/1‑58 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:2986724/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:1029492/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:1183518/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:1360518/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:737843/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:1452275/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:1611452/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:565986/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:419927/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:2628509/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:2117780/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:2812545/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:2141375/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:2594231/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTCAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:2668988/1‑69 (MQ=255)
                                        agcaAAAGCCATTGGTATTGATATTGATCCGCAGGCGATTAAGGCCAGCCGCGACAACGCTGAACGTaa                        >  1:1428918/1‑69 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      >  1:785658/1‑51 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      >  1:1389754/1‑51 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      >  1:1443255/1‑51 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      >  1:3123034/1‑51 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      >  1:1643738/1‑51 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      >  1:3234379/1‑51 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGAt                                      >  1:3246242/1‑51 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGc                    >  1:1981995/1‑69 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGc                    >  1:3360304/1‑69 (MQ=255)
                                            aaaGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGc                    >  1:1982804/1‑69 (MQ=255)
                                                     ggTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGAc           >  1:760232/1‑69 (MQ=255)
                                                              atCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATgcg                    >  1:2865622/1‑49 (MQ=255)
                                                              atCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGaa  >  1:657575/1‑69 (MQ=255)
                                                              atCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGaa  >  1:787211/1‑69 (MQ=255)
                                                              atCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGaa  >  1:740937/1‑69 (MQ=255)
                                                              atCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGaa  >  1:2601749/1‑69 (MQ=255)
                                                              atCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGaa  >  1:1978515/1‑69 (MQ=255)
                                                              atCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGaa  >  1:3282971/1‑69 (MQ=255)
                                                              atCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGa   >  1:2271410/1‑68 (MQ=255)
                                                                |                                                                  
GTTCCGGCATTCTGGCGATCGCGGCGCTGAAACTGGGTGCAGCAAAAGCCATTGGTATTGATATCGATCCGCAGGCGATTCAGGCCAGCCGCGATAACGCCGAACGTAATGGCGTTTCTGACCGTCTGGAA  >  minE/2224854‑2224984

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