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 2,065,007 T→G 8.2% V416V (GTT→GTG)  rpoD → RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,065,0070TG 8.2% 321.0 / 20.1 122V416V (GTT→GTG) rpoDRNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (67/45);  new base G (8/2);  total (75/47)
Fisher's exact test for biased strand distribution p-value = 3.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

Only 100 of 126 total aligned reads displayed.

CACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCG  >  minE/2064941‑2065073
                                                                  |                                                                  
cacCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                <  1:1647461/71‑1 (MQ=255)
 acCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaa                                                               <  1:4754065/71‑1 (MQ=255)
     aCCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                <  1:3518716/66‑1 (MQ=255)
     aCCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                <  1:1577864/66‑1 (MQ=255)
      ccGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                <  1:2650053/65‑1 (MQ=255)
         tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:1216528/71‑1 (MQ=255)
         tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:3085226/71‑1 (MQ=255)
         tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:1285275/71‑1 (MQ=255)
         tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAAt                                                       <  1:2268039/71‑1 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:3951664/1‑71 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:4756893/1‑71 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:1623571/1‑71 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:1575573/1‑71 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:1420719/1‑71 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAc                                                     >  1:1426723/1‑71 (MQ=255)
                    tCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            >  1:2204377/1‑71 (MQ=255)
                     ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            >  1:425082/1‑70 (MQ=255)
                     ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            >  1:4955241/1‑70 (MQ=255)
                      cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                          <  1:924103/55‑1 (MQ=255)
                          aCCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      <  1:2093895/71‑1 (MQ=255)
                           ccTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      <  1:2491365/70‑1 (MQ=255)
                           ccTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                     <  1:1108804/71‑3 (MQ=12)
                            cTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGtt                                    <  1:618086/71‑1 (MQ=255)
                             tGATCCAGGAAGGCAATATCGGCCTGATGAAGGCTGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                     <  1:2569484/69‑3 (MQ=9)
                              gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGt                                               >  1:2818843/1‑58 (MQ=255)
                              gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:2829745/1‑66 (MQ=255)
                              gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:491083/1‑66 (MQ=255)
                                ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            <  1:4595197/59‑1 (MQ=255)
                                ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            <  1:1495372/59‑1 (MQ=255)
                                ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                <  1:4621225/71‑1 (MQ=255)
                                ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                <  1:948051/71‑1 (MQ=255)
                                ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                <  1:1625803/71‑1 (MQ=255)
                                 tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:1851902/1‑40 (MQ=255)
                                 tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:393144/1‑40 (MQ=255)
                                 tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:1587890/1‑40 (MQ=255)
                                 tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:2681223/1‑40 (MQ=255)
                                 tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:4147094/1‑40 (MQ=255)
                                 tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:60001/1‑40 (MQ=255)
                                 tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                              >  1:5027191/1‑40 (MQ=255)
                                 ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcga                               >  1:2428536/2‑69 (MQ=255)
                                 ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcga                               >  1:3170143/2‑69 (MQ=255)
                                 acAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGt                                            >  1:1878456/2‑58 (MQ=255)
                                     gAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        <  1:371870/58‑1 (MQ=255)
                                     gAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        <  1:2026326/58‑1 (MQ=255)
                                      aaGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        <  1:3690460/57‑1 (MQ=255)
                                      aaGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTAc                          >  1:2511348/1‑71 (MQ=255)
                                       aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCtg                           >  1:1743491/1‑68 (MQ=255)
                                       aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                           >  1:2254085/1‑69 (MQ=255)
                                       aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                           >  1:5043968/1‑69 (MQ=255)
                                       aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                           >  1:1291949/1‑69 (MQ=255)
                                       aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTATCCACCTa                           >  1:1578098/1‑69 (MQ=255)
                                            aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                    >  1:4898665/1‑71 (MQ=255)
                                            aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                    >  1:991692/1‑71 (MQ=255)
                                             taTCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAAtt                                    >  1:2656642/2‑54 (MQ=255)
                                             taTCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAAtt                                    >  1:4970356/2‑54 (MQ=255)
                                             taTCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAAtt                                    >  1:75893/2‑54 (MQ=255)
                                             cATCGTTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                   <  1:483579/71‑1 (MQ=255)
                                             cATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                   <  1:483580/71‑1 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:3117681/1‑50 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:2774363/1‑50 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:3230415/1‑50 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                       >  1:2294084/1‑50 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        >  1:4060350/1‑49 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        >  1:72336/1‑49 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                 >  1:3295095/1‑56 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                 >  1:3423525/1‑56 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                        >  1:813768/1‑65 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                        >  1:1390675/1‑65 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                        >  1:2513981/1‑65 (MQ=255)
                                               tCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtgg                 <  1:3119972/71‑1 (MQ=255)
                                                cGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                        <  1:126012/47‑1 (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                                            <  1:2316836/38‑1 (MQ=255)
                                                     tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGt                                            <  1:3878127/38‑1 (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)
                                                       atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATcc          >  1:3176972/1‑70 (MQ=255)
                                                       atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATcc          <  1:2333211/70‑1 (MQ=255)
                                                       atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATcc          <  1:2991830/70‑1 (MQ=255)
                                                       atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCg         >  1:523219/1‑71 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:204568/1‑40 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:2045447/1‑40 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:2190888/1‑40 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:5114657/1‑40 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:2001162/1‑40 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:4143497/1‑40 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:4738799/1‑40 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                      >  1:2834245/1‑40 (MQ=255)
                                                          aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt        >  1:1267602/1‑69 (MQ=255)
                                                          aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt        >  1:3969095/1‑69 (MQ=255)
                                                           aaGCGGTTGATAAATTCGAATACCGCCGTTGTTACAAGTTCTcc                                <  1:1189966/44‑1 (MQ=255)
                                                             gCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGc   <  1:875616/71‑1 (MQ=255)
                                                                 ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                            <  1:4622198/42‑1 (MQ=255)
                                                                 ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                            <  1:868206/42‑1 (MQ=255)
                                                                 ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt        <  1:2898550/62‑1 (MQ=255)
                                                                  |                                                                  
CACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCG  >  minE/2064941‑2065073

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