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 R2 251 90.0 5200563 86.9% 4519289 59.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,065,013 A→G 5.2% K418K (AAA→AAG)  rpoD → RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,065,0130AG 5.2% 345.2 / 6.6 115K418K (AAA→AAG) rpoDRNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base A (69/40);  new base G (4/2);  total (73/42)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

Only 100 of 122 total aligned reads displayed.

TGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCG  >  minE/2064950‑2065073
                                                               |                                                            
tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:3085226/71‑1 (MQ=255)
tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:2571706/71‑1 (MQ=255)
tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:1216528/71‑1 (MQ=255)
tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:2272023/71‑1 (MQ=255)
tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:2268039/71‑1 (MQ=255)
tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:1285275/71‑1 (MQ=255)
  gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:4756893/1‑71 (MQ=255)
  gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:3951664/1‑71 (MQ=255)
  gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:1623571/1‑71 (MQ=255)
  gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:1426723/1‑71 (MQ=255)
  gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:1420719/1‑71 (MQ=255)
            ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            >  1:425082/1‑70 (MQ=255)
             cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                          <  1:924103/55‑1 (MQ=255)
              ttGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTa                                          >  1:5009297/1‑70 (MQ=255)
               tGACCTGATTCAGGAAGGCAAAATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTAc                                         >  1:1820771/1‑70 (MQ=255)
                 aCCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      <  1:2093895/71‑1 (MQ=255)
                  ccTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      <  1:2491365/70‑1 (MQ=255)
                  ccTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                     <  1:1108804/71‑3 (MQ=12)
                    tGATCCAGGAAGGCAATATCGGCCTGATGAAGGCTGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                     <  1:2569484/69‑3 (MQ=9)
                     gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGt                                               >  1:2818843/1‑58 (MQ=255)
                     gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:491083/1‑66 (MQ=255)
                     gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:2829745/1‑66 (MQ=255)
                       ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            <  1:1495372/59‑1 (MQ=255)
                       ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            <  1:4595197/59‑1 (MQ=255)
                       ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                <  1:1625803/71‑1 (MQ=255)
                       ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                <  1:948051/71‑1 (MQ=255)
                       ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                <  1:4621225/71‑1 (MQ=255)
                        tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:393144/1‑40 (MQ=255)
                        tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:4147094/1‑40 (MQ=255)
                        tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:5027191/1‑40 (MQ=255)
                        tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:60001/1‑40 (MQ=255)
                        tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:1851902/1‑40 (MQ=255)
                        tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:1587890/1‑40 (MQ=255)
                        ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcga                               >  1:2428536/2‑69 (MQ=255)
                        ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcga                               >  1:3173542/2‑69 (MQ=255)
                        ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcga                               >  1:3170143/2‑69 (MQ=255)
                        acAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGt                                            >  1:1878456/2‑58 (MQ=255)
                            gAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        <  1:2127057/58‑1 (MQ=255)
                             aaGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        <  1:3690460/57‑1 (MQ=255)
                              aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                           >  1:5043968/1‑69 (MQ=255)
                              aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                           >  1:2254085/1‑69 (MQ=255)
                              aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                           >  1:1291949/1‑69 (MQ=255)
                              aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTATCCACCTa                           >  1:1578098/1‑69 (MQ=255)
                                   aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                    >  1:991692/1‑71 (MQ=255)
                                   aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                    >  1:4898665/1‑71 (MQ=255)
                                   aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                    <  1:3107784/71‑1 (MQ=255)
                                    taTCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAAtt                                    >  1:4970356/2‑54 (MQ=255)
                                    taTCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAAtt                                    >  1:2656642/2‑54 (MQ=255)
                                    taTCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAAtt                                    >  1:75893/2‑54 (MQ=255)
                                    cATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                   <  1:483580/71‑1 (MQ=255)
                                    cATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                   <  1:4866391/71‑1 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:2294084/1‑50 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:2774363/1‑50 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:742241/1‑50 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:3728995/1‑50 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        >  1:72336/1‑49 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        >  1:4060350/1‑49 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                 >  1:3423525/1‑56 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                 >  1:3295095/1‑56 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                 >  1:1387133/1‑56 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                        >  1:813768/1‑65 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                        >  1:2513981/1‑65 (MQ=255)
                                     aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATAACGCCGTGGTTACAAGTtctc                                 >  1:5133367/1‑56 (MQ=255)
                                      tCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtgg                 <  1:3119972/71‑1 (MQ=255)
                                       cGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        <  1:126012/47‑1 (MQ=255)
                                          tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGa             <  1:2469570/71‑1 (MQ=255)
                                           cTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                            >  1:4496882/1‑55 (MQ=255)
                                           cTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGAt            >  1:1189773/1‑71 (MQ=255)
                                           cTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTATCCACCTACGCAACCTGGTGGAt            >  1:5067196/1‑71 (MQ=255)
                                            tgatgaAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAATTCTAGACCTATGCGACGTGGTGCAtt           >  1:4832722/1‑70 (MQ=255)
                                            tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            <  1:3878127/38‑1 (MQ=255)
                                            tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            <  1:1532944/38‑1 (MQ=255)
                                            tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                     >  1:2689457/1‑61 (MQ=255)
                                            tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                     >  1:3162790/1‑61 (MQ=255)
                                            tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATc           >  1:3301009/1‑71 (MQ=255)
                                              atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGtt                                    >  1:4831013/1‑44 (MQ=255)
                                              atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGt                                     >  1:4011548/1‑43 (MQ=255)
                                              atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATcc          <  1:2333211/70‑1 (MQ=255)
                                              atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATcc          >  1:3176972/1‑70 (MQ=255)
                                              atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATcc          <  1:2991830/70‑1 (MQ=255)
                                              atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCg         >  1:523219/1‑71 (MQ=255)
                                                gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:4738799/1‑40 (MQ=255)
                                                gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:2001162/1‑40 (MQ=255)
                                                gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:2834245/1‑40 (MQ=255)
                                                gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:4143497/1‑40 (MQ=255)
                                                gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:2190888/1‑40 (MQ=255)
                                                gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:204568/1‑40 (MQ=255)
                                                gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:2045447/1‑40 (MQ=255)
                                                 aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt        >  1:1267602/1‑69 (MQ=255)
                                                  aaGCGGTTGATAAATTCGAATACCGCCGTTGTTACAAGTTCTcc                                <  1:1189966/44‑1 (MQ=255)
                                                     cGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCg  <  1:1617499/71‑1 (MQ=255)
                                                        ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                            <  1:4622198/42‑1 (MQ=255)
                                                        ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                            <  1:868206/42‑1 (MQ=255)
                                                        ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                            <  1:877670/42‑1 (MQ=255)
                                                        ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt        <  1:2898550/62‑1 (MQ=255)
                                                           aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa      >  1:616585/1‑61 (MQ=255)
                                                           aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa      >  1:4811615/1‑61 (MQ=255)
                                                           aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa      >  1:2426196/1‑61 (MQ=255)
                                                           aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa      >  1:3553761/1‑61 (MQ=255)
                                                           aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa      >  1:1089195/1‑61 (MQ=255)
                                                               |                                                            
TGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCG  >  minE/2064950‑2065073

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