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 2,065,034 C→T 7.7% Y425Y (TAC→TAT)  rpoD → RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,065,0340CT 7.7% 362.4 / 13.7 117Y425Y (TAC→TAT) rpoDRNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base C (63/45);  new base T (7/2);  total (70/47)
Fisher's exact test for biased strand distribution p-value = 3.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.30e-01

Only 100 of 125 total aligned reads displayed.

TGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCA  >  minE/2064965‑2065104
                                                                     |                                                                      
tGACCTGATTCAGGAAGGCAAAATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTAc                                                                        >  1:1820771/1‑70 (MQ=255)
   ccTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                                                    <  1:1108804/71‑3 (MQ=12)
     tGATCCAGGAAGGCAATATCGGCCTGATGAAGGCTGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                                                    <  1:2569484/69‑3 (MQ=9)
        ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                                               <  1:948051/71‑1 (MQ=255)
        ttCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                                               <  1:1625803/71‑1 (MQ=255)
         ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcga                                                              >  1:2428536/2‑69 (MQ=255)
         ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcga                                                              >  1:3173542/2‑69 (MQ=255)
         ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcga                                                              >  1:3170143/2‑69 (MQ=255)
             gAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                                                       <  1:2026326/58‑1 (MQ=255)
             gAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                                                       <  1:2127057/58‑1 (MQ=255)
             gAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                                                       <  1:371870/58‑1 (MQ=255)
              aaGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                                                       <  1:3690460/57‑1 (MQ=255)
              aaGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTAc                                                         >  1:2511348/1‑71 (MQ=255)
               aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCtg                                                          >  1:1743491/1‑68 (MQ=255)
               aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                                                          >  1:1291949/1‑69 (MQ=255)
               aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                                                          >  1:2254085/1‑69 (MQ=255)
               aGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTa                                                          >  1:5043968/1‑69 (MQ=255)
                    aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                                                   <  1:3107784/71‑1 (MQ=255)
                    aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                                                   >  1:4898665/1‑71 (MQ=255)
                    aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                                                   >  1:991692/1‑71 (MQ=255)
                     taTCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAAtt                                                                   >  1:4970356/2‑54 (MQ=255)
                     taTCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAAtt                                                                   >  1:2656642/2‑54 (MQ=255)
                     cATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                                                  <  1:483580/71‑1 (MQ=255)
                     cATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                                                  <  1:4866391/71‑1 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                                                      >  1:3230415/1‑50 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                                                      >  1:2881537/1‑50 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                                                      >  1:742241/1‑50 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                                                      >  1:3117681/1‑50 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaa                                                                      >  1:2774363/1‑50 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACa                                                                       >  1:72336/1‑49 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                                                >  1:1387133/1‑56 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                                                >  1:3423525/1‑56 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtctc                                                                >  1:3295095/1‑56 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                                                       >  1:2513981/1‑65 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                                                       >  1:1390675/1‑65 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                                                       >  1:813768/1‑65 (MQ=255)
                      aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATAACGCCGTGGTTACAAGTtctc                                                                >  1:5133367/1‑56 (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)
                             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)
                               atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCg                                        >  1:523219/1‑71 (MQ=255)
                                 gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                                                     >  1:4143497/1‑40 (MQ=255)
                                 gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                                                     >  1:4428889/1‑40 (MQ=255)
                                 gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                                                     >  1:2834245/1‑40 (MQ=255)
                                 gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                                                     >  1:2190888/1‑40 (MQ=255)
                                 gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                                                     >  1:204568/1‑40 (MQ=255)
                                 gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAg                                                                     >  1:2045447/1‑40 (MQ=255)
                                  aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt                                       >  1:3969095/1‑69 (MQ=255)
                                   aaGCGGTTGATAAATTCGAATACCGCCGTTGTTACAAGTTCTcc                                                               <  1:1189966/44‑1 (MQ=255)
                                     gCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGc                                  <  1:875616/71‑1 (MQ=255)
                                      cGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCg                                 <  1:1617499/71‑1 (MQ=255)
                                         ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                                           <  1:868206/42‑1 (MQ=255)
                                         ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                                           <  1:4622198/42‑1 (MQ=255)
                                         ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt                                       <  1:2898550/62‑1 (MQ=255)
                                            aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa                                     >  1:616585/1‑61 (MQ=255)
                                            aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa                                     >  1:4811615/1‑61 (MQ=255)
                                            aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa                                     >  1:1089195/1‑61 (MQ=255)
                                            aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa                                     >  1:2426196/1‑61 (MQ=255)
                                            aTAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCa                                     >  1:3553761/1‑61 (MQ=255)
                                                   cGAATACCGCCGTGGTTACAAGTTCTCCATCTACGCAACCTGGTGGATc                                          >  1:704683/1‑49 (MQ=255)
                                                   cGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATc                                          >  1:3770414/1‑49 (MQ=255)
                                                   cGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATc                                          >  1:887585/1‑49 (MQ=255)
                                                   cGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATc                                          >  1:855779/1‑49 (MQ=255)
                                                   cGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGctct                     <  1:4056713/70‑1 (MQ=255)
                                                   cGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGctct                     <  1:1551437/70‑1 (MQ=255)
                                                   cGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGctct                     <  1:4400454/70‑1 (MQ=255)
                                                             cttGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCa          <  1:2055846/69‑1 (MQ=255)
                                                             cgTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGTTCTATCGCGGATCa          <  1:3015837/71‑1 (MQ=255)
                                                             cgTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGTTCTATCGCGGATCa          <  1:3021800/71‑1 (MQ=255)
                                                             cgTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCa          <  1:2707594/71‑1 (MQ=255)
                                                              gTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGTTCTATCGCGGATCa          <  1:2621516/70‑1 (MQ=255)
                                                               tGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATc           <  1:1108133/68‑1 (MQ=255)
                                                               tGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATc           <  1:480481/68‑1 (MQ=255)
                                                                 gTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGgc       <  1:4700273/70‑1 (MQ=255)
                                                                 gTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGgc       <  1:663913/70‑1 (MQ=255)
                                                                  ttACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGctct                     <  1:5067144/55‑1 (MQ=255)
                                                                   tACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGa             <  1:1713656/62‑1 (MQ=255)
                                                                   tACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGa             <  1:4838265/62‑1 (MQ=255)
                                                                   tACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGgcgc     <  1:5166803/70‑1 (MQ=255)
                                                                    aCAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGgcgcg    <  1:3698176/70‑1 (MQ=255)
                                                                    aCAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGgcgcg    >  1:1962679/1‑70 (MQ=255)
                                                                    aCAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGgcgcg    >  1:928816/1‑70 (MQ=255)
                                                                    aCAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGgcgcg    >  1:1243160/1‑70 (MQ=255)
                                                                    aCAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGgcgc     >  1:1775864/1‑69 (MQ=255)
                                                                     cAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATc                              >  1:2200297/1‑43 (MQ=255)
                                                                     cAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATc                              >  1:4722932/1‑43 (MQ=255)
                                                                     cAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATc                              >  1:1935601/1‑43 (MQ=255)
                                                                     cAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATc                              >  1:4649150/1‑43 (MQ=255)
                                                                     cAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATc                              >  1:3175789/1‑43 (MQ=255)
                                                                     cAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATc                              >  1:1125527/1‑43 (MQ=255)
                                                                     cAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCa  >  1:2958889/1‑71 (MQ=255)
                                                                     |                                                                      
TGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCA  >  minE/2064965‑2065104

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