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 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,716,835 G→T 28.6% intergenic (+93/+105) yphH → / ← glyA predicted DNA‑binding transcriptional regulator/serine hydroxymethyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,716,8350GT28.6% 107.3 / 48.9 93intergenic (+93/+105)yphH/glyApredicted DNA‑binding transcriptional regulator/serine hydroxymethyltransferase
Reads supporting (aligned to +/- strand):  ref base G (33/17);  new base T (11/13);  total (52/41)
Fisher's exact test for biased strand distribution p-value = 1.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

Only 100 of 104 total aligned reads displayed.

CCCGAAGGAAGCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAT  >  minE/1716767‑1716902
                                                                    |                                                                   
cccGAAGGAAGCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGga                                                                    <  1:1278834/70‑1 (MQ=255)
   gaaggaagCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGga                                                                    >  1:4538483/1‑67 (MQ=255)
       gaagCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGc                                                              <  1:830322/69‑1 (MQ=255)
       gaagCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCaa                                                            <  1:4219521/71‑1 (MQ=255)
       gaagCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCaa                                                            <  1:1382750/71‑1 (MQ=255)
              tgatgaTCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATAtt                                                      >  1:5167321/1‑70 (MQ=255)
              tgatgaTCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATAtt                                                      >  1:2158306/1‑70 (MQ=255)
                   atCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGc                                                              <  1:1722259/57‑1 (MQ=255)
                   atCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGc                                                              <  1:4501282/57‑1 (MQ=255)
                    tCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGa                                                    >  1:5353944/1‑66 (MQ=255)
                    tCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTg                                               >  1:2183963/1‑71 (MQ=255)
                     cATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAAttt                                                >  1:2209273/1‑69 (MQ=255)
                     cATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAAttt                                                >  1:2953982/1‑69 (MQ=255)
                     cATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAAttt                                                >  1:1408933/1‑69 (MQ=255)
                     cATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAAttt                                                >  1:4539410/1‑69 (MQ=255)
                     cATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTg                                               >  1:4178114/1‑70 (MQ=255)
                      aTAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAAttt                                                >  1:294353/1‑68 (MQ=255)
                       tAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAatatat                                                       <  1:1149807/60‑1 (MQ=255)
                        aaaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGgaga                                                                  >  1:5673330/1‑48 (MQ=255)
                         aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACgg                                                                     >  1:4679555/1‑44 (MQ=255)
                         aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTg                                                     >  1:2996130/1‑60 (MQ=255)
                         aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTg                                                     >  1:4525507/1‑60 (MQ=255)
                         aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAg                                          >  1:5357842/1‑71 (MQ=255)
                         aaCGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAg                                          >  1:621064/1‑71 (MQ=255)
                              caaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTg                                     <  1:1355129/70‑1 (MQ=11)
                              caaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTg                                     <  1:1070969/70‑1 (MQ=11)
                              caaaTTGCCTCATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTg                                     <  1:4129553/70‑1 (MQ=11)
                              aaaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAatatat                                                       >  1:4963288/1‑53 (MQ=255)
                               agcttgcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTg                                               >  1:4318637‑M2/20‑60 (MQ=255)
                               agcttgcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg                                     <  1:334856‑M2/51‑1 (MQ=255)
                               agcttgcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg                                     <  1:345139‑M2/51‑1 (MQ=255)
                               aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGgaga                                                                  >  1:4091429/1‑41 (MQ=40)
                               aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGgaga                                                                  >  1:3653164/1‑41 (MQ=40)
                               aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGgaga                                                                  >  1:3717694/1‑41 (MQ=40)
                               aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGgaga                                                                  >  1:1479918/1‑41 (MQ=40)
                               aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGgaga                                                                  >  1:1042618/1‑41 (MQ=40)
                               aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTg                                     >  1:1029988/1‑70 (MQ=11)
                               aaaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGt                                    <  1:1405716/71‑1 (MQ=11)
                                gcttgcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg                                     >  1:100149‑M2/19‑69 (MQ=255)
                                aaTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt                                    <  1:1965428/70‑1 (MQ=255)
                                aaTTGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGt                                    <  1:1123517/70‑1 (MQ=11)
                                 aTTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAg                                  <  1:280107/71‑1 (MQ=255)
                                  ttgcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAata                                                          <  1:829910‑M2/30‑1 (MQ=255)
                                  ttGCCTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAg                                  >  1:4964856/1‑70 (MQ=11)
                                    gcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAatata                                                        >  1:24882‑M2/15‑46 (MQ=255)
                                    gcctgatgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAatata                                                        >  1:3719605‑M2/15‑46 (MQ=255)
                                     ccTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAggac                               <  1:3626879/70‑3 (MQ=11)
                                     ccTGATGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga                                <  1:5333843/69‑2 (MQ=11)
                                       tGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGa                            >  1:87508/1‑71 (MQ=255)
                                        gATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAAt                                                  <  1:3524256/48‑1 (MQ=255)
                                         atgcgcgatGCTTATCAGGCCTACCAGAAGATTGCa                                                             >  1:4517591‑M2/10‑36 (MQ=255)
                                         atgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATa                          <  1:276209‑M2/62‑1 (MQ=255)
                                         atgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATa                          <  1:5482606‑M2/62‑1 (MQ=255)
                                         aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt                                    >  1:5241154/1‑61 (MQ=255)
                                         aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt                                    >  1:3472443/1‑61 (MQ=255)
                                         aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt                                    >  1:3465622/1‑61 (MQ=255)
                                         aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGa                            <  1:64705/69‑1 (MQ=255)
                                         aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt                           <  1:5506823/70‑1 (MQ=255)
                                         aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt                           <  1:1271959/70‑1 (MQ=255)
                                         aTGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGAt                           <  1:1233144/70‑1 (MQ=11)
                                         aTGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATa                          <  1:2054670/71‑1 (MQ=11)
                                          tgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg                                     <  1:5484282‑M2/51‑1 (MQ=255)
                                          tgcgcgatGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTg                                     <  1:303370‑M2/51‑1 (MQ=255)
                                            cgcgatGCTTATCAGGCCTACCAGAAGATTGCAata                                                          >  1:4175209‑M2/7‑36 (MQ=255)
                                            cgcTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAgg                       >  1:1208984/1‑71 (MQ=255)
                                            cgcTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAg                        <  1:3703517/70‑1 (MQ=11)
                                            cgcTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAg                        <  1:4010410/70‑1 (MQ=11)
                                              cgatGCTTATCAGGCCTACA‑GAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGt                    <  1:2714889‑M2/67‑1 (MQ=255)
                                                atGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGtttt                                      <  1:5031911‑M2/50‑1 (MQ=255)
                                                atGCTTATCAGGCCTACCAGAAGATAGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGtt                   <  1:4203362‑M2/69‑1 (MQ=255)
                                                aCGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGa                            >  1:1349458/1‑62 (MQ=255)
                                                aCGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGa                            >  1:4984271/1‑62 (MQ=255)
                                                aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga                                >  1:5119812/1‑57 (MQ=2)
                                                aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga                                >  1:293058/1‑57 (MQ=2)
                                                aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga                                >  1:5616760/1‑57 (MQ=2)
                                                aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga                                >  1:4816340/1‑57 (MQ=2)
                                                aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCgct                   >  1:4413369/1‑69 (MQ=2)
                                                aCGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCgct                   >  1:1436366/1‑69 (MQ=2)
                                                 cGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCaaa                                           >  1:1220582/1‑46 (MQ=255)
                                                 cGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGtt                   <  1:5436240/70‑1 (MQ=255)
                                                   cTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCa                 >  1:2513460/1‑70 (MQ=255)
                                                   cTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCa                 >  1:4071410/1‑70 (MQ=255)
                                                   cTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCAc                >  1:3248722/1‑71 (MQ=255)
                                                   cTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATATGCGATGTTTTGTAGGACTGATAAGGCGCTcg                 >  1:5395870/1‑69 (MQ=2)
                                                     tATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAgga                                >  1:109984/1‑52 (MQ=2)
                                                      aTCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTcgcg               <  1:3798215/69‑1 (MQ=2)
                                                       tCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTa                                   <  1:4110570/48‑1 (MQ=11)
                                                         aGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAgg                                 >  1:3164094/1‑48 (MQ=11)
                                                         aGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAgg                                 >  1:3956611/1‑48 (MQ=11)
                                                            ccTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt                           <  1:5218794/51‑1 (MQ=255)
                                                              tACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa                          <  1:529082/50‑1 (MQ=255)
                                                              tACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa                          <  1:1792834/50‑1 (MQ=255)
                                                                cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGt                                    >  1:5162570/1‑38 (MQ=255)
                                                                cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATaa                         >  1:1550923/1‑49 (MQ=255)
                                                                cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAg                        >  1:1556834/1‑50 (MQ=255)
                                                                cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAg                        >  1:4125468/1‑50 (MQ=255)
                                                                cacGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCgg     <  1:5050166/69‑1 (MQ=255)
                                                                 acGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATaa                         >  1:5061555/1‑48 (MQ=255)
                                                                 acGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAt  >  1:5566762/1‑71 (MQ=255)
                                                                   ggAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc                      >  1:3973499/1‑49 (MQ=255)
                                                                    |                                                                   
CCCGAAGGAAGCCTTGATGATCATAAACGAAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAT  >  minE/1716767‑1716902

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