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 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,302,608 T→C 57.1% K158R (AAG→AGG)  dacD ← D‑alanyl‑D‑alanine carboxypeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,302,6080TC57.1% 59.2 / 151.3 119K158R (AAG→AGG) dacDD‑alanyl‑D‑alanine carboxypeptidase
Reads supporting (aligned to +/- strand):  ref base T (27/24);  new base C (27/41);  total (54/65)
Fisher's exact test for biased strand distribution p-value = 1.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

Only 100 of 122 total aligned reads displayed.

CCGAGCTATGCTGGCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAATATAGTCAGCCAGAG  >  minE/1302540‑1302674
                                                                    |                                                                  
 cGAGCTATGCTGGCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCctct                                                                 <  1:2182264/71‑1 (MQ=255)
 cGAGCTATGCTGGCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCctct                                                                 <  1:1557524/71‑1 (MQ=255)
   aGCTATGCTGGCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCg                                                               >  1:617730/1‑71 (MQ=255)
    gCTATGCTGGCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCg                                                               <  1:2189956/70‑1 (MQ=255)
       aTGCTGGCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCa                                                            >  1:825375/1‑70 (MQ=255)
       aTGCTGGCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCa                                                            >  1:56948/1‑70 (MQ=255)
            ggCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGc                                                             >  1:1520830/1‑64 (MQ=255)
            ggCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGc                                                             >  1:3471469/1‑64 (MQ=255)
            ggCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGc                                                             >  1:2938910/1‑64 (MQ=255)
            ggCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCAt                                                           >  1:2259044/1‑66 (MQ=255)
             gCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAg                                                         <  1:2697169/67‑1 (MQ=255)
             gCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAg                                                         <  1:2436242/67‑1 (MQ=255)
             gCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAg                                                         <  1:3334635/67‑1 (MQ=255)
             gCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAg                                                         <  1:1909612/67‑1 (MQ=255)
             gCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAg                                                         <  1:2204596/67‑1 (MQ=255)
             gCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAg                                                         <  1:2353440/67‑1 (MQ=255)
               cAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGc                                                             >  1:615637/1‑61 (MQ=255)
               cAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAgtt                                                       >  1:2598460/1‑67 (MQ=255)
                     cATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCAtt                                             <  1:1372523/71‑1 (MQ=255)
                     cATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCAtt                                             <  1:3423641/71‑1 (MQ=255)
                       tCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGTGATGCAGCTTCTCGGCATAg                                                         <  1:941405/57‑1 (MQ=255)
                       tCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAg                                                         <  1:2869200/57‑1 (MQ=255)
                        ccAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTc                                           >  1:2305511/1‑70 (MQ=255)
                         cAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTca                                          <  1:3322182/70‑1 (MQ=255)
                         cAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCtctc                                                                >  1:1046427/1‑48 (MQ=255)
                          aGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTAGGCATAGTTGTTCATCAtt                                             >  1:3154702/1‑66 (MQ=255)
                          aGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTcaa                                         >  1:2177228/1‑70 (MQ=255)
                          aGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTca                                          >  1:25286/1‑69 (MQ=255)
                           gACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:1781591/71‑1 (MQ=255)
                           gACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTcaac                                        >  1:3452317/1‑70 (MQ=255)
                           gACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTcaac                                        >  1:2889328/1‑70 (MQ=255)
                            aCCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTcaacaa                                      <  1:2553424/71‑1 (MQ=255)
                            aCCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTcaacaa                                      <  1:2842602/71‑1 (MQ=255)
                            aCCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTcaacaa                                      <  1:729636/71‑1 (MQ=255)
                               aTGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCgg                                                              <  1:3519511/44‑1 (MQ=255)
                                  cACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGc                                 <  1:3505518/70‑1 (MQ=255)
                                  cACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGc                                 <  1:1811226/70‑1 (MQ=255)
                                  cACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGc                                 <  1:1046343/70‑1 (MQ=255)
                                  cACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGc                                 <  1:2569473/70‑1 (MQ=255)
                                  cACTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGc                                 <  1:247691/70‑1 (MQ=255)
                                    cTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGt                              <  1:3633801/71‑1 (MQ=255)
                                    cTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGt                              <  1:2798185/71‑1 (MQ=255)
                                    cTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGt                              <  1:1175391/71‑1 (MQ=255)
                                    cTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGt                              <  1:1339990/71‑1 (MQ=255)
                                    cTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGt                              <  1:2483759/71‑1 (MQ=255)
                                    cTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGt                              <  1:3046361/71‑1 (MQ=255)
                                    cTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGt                              <  1:1777534/71‑1 (MQ=255)
                                    cTGTTTCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGt                              <  1:3554347/71‑1 (MQ=255)
                                     tGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGtt                             >  1:91098/1‑71 (MQ=255)
                                       tttCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGc                           <  1:3334875/71‑1 (MQ=255)
                                       tttCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGc                           >  1:3713419/1‑71 (MQ=255)
                                       tttCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGc                           >  1:2811512/1‑71 (MQ=255)
                                        ttCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAg                                                         >  1:1420998/1‑40 (MQ=255)
                                        ttCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAg                                                         >  1:3350712/1‑40 (MQ=255)
                                         tCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:2350537/57‑1 (MQ=255)
                                         tCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:1326320/57‑1 (MQ=255)
                                         tCAAAATGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTcaaca                                       >  1:1152912/1‑57 (MQ=255)
                                           aaaaTGCGTATCCTTGAGATGCAGCCTCTCGGCATAgttgtt                                                    >  1:339093/1‑42 (MQ=255)
                                           aaaaTGCGTATCCTTGAGATGCAGCCTCTCGGCATAgttgtt                                                    >  1:1924425/1‑42 (MQ=255)
                                           aaaaTGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCAc                       >  1:2533232/1‑71 (MQ=255)
                                            aaaTGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGccc                         <  1:2681693/68‑1 (MQ=255)
                                             aaTGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCg                     <  1:2583769/71‑1 (MQ=255)
                                             aaTGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCg                     <  1:427153/71‑1 (MQ=255)
                                             aaTGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTtcatc                                                <  1:3543510/44‑1 (MQ=255)
                                             aaTGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTtcatc                                                <  1:2671851/44‑1 (MQ=255)
                                             aaTGCGTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCg                     <  1:1858577/71‑1 (MQ=255)
                                              aTGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCAc                       >  1:1650457/1‑68 (MQ=255)
                                              aTGCGTATCCTTGAGATGCAGCCTCTCGGCATAgttgtt                                                    >  1:3208250/1‑39 (MQ=255)
                                              aTGCGTATCCTTGAGATGCAGCCTCTCGGCATAgttgtt                                                    >  1:1392856/1‑39 (MQ=255)
                                              aTGCGTATCCTTGAGATGCAGCCTCTCGGCATAgttgtt                                                    >  1:576713/1‑39 (MQ=255)
                                              aTGCGTATCCTTGAGATGCAGCCTCTCGGCATAgttgtt                                                    >  1:2740245/1‑39 (MQ=255)
                                              aTGAGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCa                        >  1:2023985/1‑67 (MQ=255)
                                                  gTATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAat                <  1:1063571/71‑1 (MQ=255)
                                                   tATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTcaacaa                                      <  1:99223/48‑1 (MQ=255)
                                                   tATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTcaacaa                                      <  1:2296465/48‑1 (MQ=255)
                                                   tATCCTTGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTcaacaa                                      <  1:2524372/48‑1 (MQ=255)
                                                     tCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTcaac                                        >  1:1840466/1‑44 (MQ=255)
                                                     tCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAAc                                    >  1:89559/1‑48 (MQ=255)
                                                     tCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACt                                   >  1:1569856/1‑49 (MQ=255)
                                                       cTTGTGATGCAGCTTCTCGGCATAGTTGTTCATCATTTcaacaa                                      >  1:2842967/1‑44 (MQ=255)
                                                       cTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAATATAGt           <  1:2290947/71‑1 (MQ=255)
                                                        ttGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAAc                                    <  1:3215493/45‑1 (MQ=255)
                                                         tGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAATATAGt           >  1:3335406/1‑69 (MQ=255)
                                                         tGAGATGCAGCTTCTCGGCATAGATGTTCATCATTTCAACAAAc                                    >  1:3657164/1‑44 (MQ=255)
                                                         tGAGATGCAGCCTCTCGGCATAGTTGTTCATCATTTc                                           <  1:1630411/37‑1 (MQ=255)
                                                           agaTGCAGCCTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:3122721/39‑1 (MQ=255)
                                                           agaTGCAGCCTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:1187555/39‑1 (MQ=255)
                                                           agaTGCAGCCTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:20692/39‑1 (MQ=255)
                                                           agaTGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAATATAGTCAg        >  1:2922133/1‑70 (MQ=255)
                                                           agaTGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAATATAGTCAGc       <  1:686534/71‑1 (MQ=255)
                                                             aTGCAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAATATAGTCAGCCa     <  1:1501618/71‑1 (MQ=255)
                                                              tGCAGCCTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:1673899/36‑1 (MQ=255)
                                                              tGCAGCCTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:754717/36‑1 (MQ=255)
                                                              tGCAGCCTCTCGGCATAGTTGTTCATCATTTcaaca                                       <  1:2681552/36‑1 (MQ=255)
                                                                cAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAAc                                    >  1:436875/1‑37 (MQ=255)
                                                                cAGCCTCTCGGCATAGTTGTTCATCATTTCAACAAAc                                    >  1:1130017/1‑37 (MQ=255)
                                                                 aGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAata               >  1:3244777/1‑57 (MQ=255)
                                                                   cTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGccc                         <  1:2255937/45‑1 (MQ=255)
                                                                   cTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGccc                         <  1:2290717/45‑1 (MQ=255)
                                                                    ttCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAATATAGTCAGCCagag  <  1:554221/67‑1 (MQ=255)
                                                                    |                                                                  
CCGAGCTATGCTGGCCAGGTGCATCCAGACCATGCACTGTTTCAAAATGCGTATCCTTGAGATGCAGCTTCTCGGCATAGTTGTTCATCATTTCAACAAACTGCCGTTGCCCACCGGCAATATAGTCAGCCAGAG  >  minE/1302540‑1302674

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