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 F3 I0 R2 88 130.8 6963722 93.6% 6518043 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,804,090 G→A 49.3% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,804,0900GA49.3% 13.6 / inf 292G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (67/81);  new base A (70/74);  total (137/155)
Fisher's exact test for biased strand distribution p-value = 6.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.04e-01

Only 100 of 297 total aligned reads displayed.

ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  minE/1804022‑1804160
                                                                    |                                                                      
aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                      <  1:1094390/71‑1 (MQ=255)
aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                      <  1:1027094/71‑1 (MQ=255)
  tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAt                                                                      >  1:1446095/1‑69 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  >  1:6873191/1‑71 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  >  1:2298246/1‑71 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:6701043/1‑71 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:13298/1‑68 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                                <  1:3009192/68‑1 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                                <  1:2007499/68‑1 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                                <  1:1678344/68‑1 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                             >  1:2866531/1‑71 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                    >  1:2958173/1‑64 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                             >  1:269823/1‑71 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                             >  1:3888072/1‑71 (MQ=255)
           catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                           >  1:463925/1‑71 (MQ=255)
            atgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                            <  1:3647631/69‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGTACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACtttgtt                                                       <  1:2060961/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       >  1:5957936/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:6910845/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:2499908/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:4936059/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:6325411/71‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGTGAATTAACGAGACGTTGttt                                                      <  1:3944745/71‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:408738/71‑1 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                   >  1:376027/1‑57 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:5617248/58‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:5897258/69‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:6244600/69‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:1560491/1‑71 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:2098108/1‑71 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    <  1:3593562/71‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:3517346/1‑71 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:6023728/1‑71 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                                   <  1:345669/71‑1 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                                   >  1:2150635/1‑70 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   >  1:4322881/1‑53 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   >  1:4471045/1‑53 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                  >  1:3512156/1‑70 (MQ=255)
                      aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                   >  1:1946463/1‑52 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:5269379/71‑1 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                  >  1:545998/1‑66 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:2363395/71‑1 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:834459/71‑1 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         <  1:2200855/71‑1 (MQ=255)
                              ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         <  1:3296568/70‑1 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:138704/1‑69 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACTTTGttt                                                      <  1:2591/54‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:2527483/54‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:4038564/54‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:4546876/54‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                       <  1:3550998/69‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:5161019/39‑1 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:308369/40‑1 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:2443838/1‑62 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:4239239/1‑62 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                         >  1:3186025/1‑48 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:6110071/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:2397306/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:1783487/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                   <  1:5508337/70‑1 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                                >  1:2751085/1‑71 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                                >  1:2120022/1‑71 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                   <  1:5012872/51‑1 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                                <  1:4214493/70‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                                >  1:6471464/1‑36 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                                >  1:4132248/1‑36 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgtt                                                          >  1:122659/1‑42 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                      <  1:1357803/46‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:2806811/53‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:5331297/56‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                            <  1:5539019/71‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                            <  1:916411/71‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                          <  1:6749207/71‑1 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:3807406/71‑1 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATCAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:1912843/71‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:866453/48‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:6155859/48‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:1182444/48‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:176731/58‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:824515/58‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                                           <  1:737753/35‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:5047670/48‑1 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:4729731/1‑48 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:5765140/1‑48 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:3228591/1‑48 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:418884/1‑48 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:5038768/1‑48 (MQ=255)
                                                    tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:1318553/70‑1 (MQ=255)
                                                    tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:417801/70‑1 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:5729622/62‑1 (MQ=255)
                                                         aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGt               <  1:6311822/69‑1 (MQ=255)
                                                         aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGGCTCAGGAAAACCACAGt               <  1:6129992/69‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:5230336/1‑62 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:4898985/1‑62 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:54145/1‑65 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa              <  1:4377025/70‑1 (MQ=255)
                                                          aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:6590833/71‑1 (MQ=255)
                                                          aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:930224/71‑1 (MQ=255)
                                                                 ggggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:4675230/52‑1 (MQ=255)
                                                                    gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTg  <  1:2427256/71‑1 (MQ=255)
                                                                    |                                                                      
ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  minE/1804022‑1804160

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