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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,677,424 T→A 35.3% Q169L (CAG→CTG)  yhgA ← predicted transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,677,4240TA35.3% 103.6 / 96.4 116Q169L (CAG→CTG) yhgApredicted transposase
Reads supporting (aligned to +/- strand):  ref base T (37/38);  new base A (13/28);  total (50/66)
Fisher's exact test for biased strand distribution p-value = 7.94e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.85e-01

Only 100 of 117 total aligned reads displayed.

AGCCCCATCAGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATAAA  >  minE/2677358‑2677484
                                                                  |                                                            
aGCCCCATCAGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGtgctgc                                                            >  1:2400906/1‑69 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACTTCGGTGCTGCATGATTtc                                                    >  1:2894614/1‑68 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGAtat                                                     >  1:87928/1‑65 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtc                                                    >  1:2293099/1‑68 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtc                                                    >  1:3164692/1‑68 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtc                                                    >  1:463798/1‑68 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtc                                                    >  1:604471/1‑68 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtc                                                    >  1:2122999/1‑68 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtc                                                    >  1:1913675/1‑68 (MQ=255)
         aGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtc                                                    >  1:1847212/1‑68 (MQ=255)
           gTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtcatc                                                 <  1:254381/69‑1 (MQ=255)
           gTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtcatc                                                 <  1:350573/69‑1 (MQ=255)
           gTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtcatc                                                 <  1:810145/69‑1 (MQ=255)
           gTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtcatc                                                 <  1:3249035/69‑1 (MQ=255)
           gTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtcatc                                                 <  1:894823/69‑1 (MQ=255)
            tCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTtcatc                                                 <  1:2419680/68‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:1074321/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:2441860/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:426336/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:2057100/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:1924963/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:1821102/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:1002023/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:3157837/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:313038/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:3034652/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:1739537/69‑1 (MQ=255)
                 ttGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:3304608/69‑1 (MQ=255)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:3001780/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:353506/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2749220/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1101831/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2737590/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2725282/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:424933/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2618146/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:3147090/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1091348/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2450721/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2925398/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1150375/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:87925/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:847937/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1710195/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1717727/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1785153/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1799360/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:891746/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1956003/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2066101/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1333296/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:611940/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:1263272/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2371166/59‑1 (MQ=39)
                  tGACGAATATGTTTTTGAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    <  1:2141119/59‑1 (MQ=39)
                   gACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGc                                          >  1:775369/1‑68 (MQ=255)
                   gACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGc                                          >  1:2006125/1‑68 (MQ=255)
                      gAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATg                                       <  1:1939696/68‑1 (MQ=255)
                          atGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:2842623/60‑1 (MQ=255)
                          atGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGt                                  <  1:1931744/69‑1 (MQ=255)
                          atGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGt                                  <  1:342585/69‑1 (MQ=255)
                          atGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGt                                  <  1:764195/69‑1 (MQ=255)
                           tGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGt                                  >  1:2994106/1‑68 (MQ=255)
                           tGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGt                                  <  1:846568/68‑1 (MQ=255)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGAtt                                                      >  1:1534061/1‑41 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:3362528/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:913802/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:3184583/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:470948/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:780852/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:2375800/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:2966591/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:2838041/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:2950237/1‑43 (MQ=38)
                                  gAATTAACTCCAGTAGAGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:234442/1‑43 (MQ=37)
                                  gAATTAAATCCAGTAGCGCCATACGTCGGTGCAGCATGATTtc                                                    >  1:2098434/1‑43 (MQ=37)
                                    aTTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAgg                                           <  1:1070289/50‑1 (MQ=255)
                                       aaCTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAg                      >  1:2907450/1‑68 (MQ=255)
                                       aaCTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAg                      >  1:2122566/1‑68 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACatcaatc                        >  1:2837297/1‑48 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACatcaatc                        >  1:2705662/1‑48 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACatcaatc                        >  1:2657248/1‑48 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACatcaatc                        >  1:1701315/1‑48 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACatcaatc                        >  1:1931346/1‑48 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACatcaatc                        >  1:1398436/1‑48 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACatcaatc                        >  1:1273298/1‑48 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGa                  >  1:1629862/1‑54 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGa                  >  1:2493953/1‑54 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGa                  >  1:639985/1‑54 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGa                  >  1:2520688/1‑54 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaa   >  1:2398757/1‑69 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaa   >  1:430535/1‑69 (MQ=255)
                                                         cGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaa   >  1:2960427/1‑69 (MQ=255)
                                                           tCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaaa  <  1:2979520/68‑1 (MQ=255)
                                                           tCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaaa  <  1:46927/68‑1 (MQ=255)
                                                           tCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaaa  <  1:3337865/68‑1 (MQ=255)
                                                           tCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaaa  <  1:1360884/68‑1 (MQ=255)
                                                           tCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaaa  <  1:1302469/68‑1 (MQ=255)
                                                           tCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaaa  <  1:3279000/68‑1 (MQ=255)
                                                           tCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATaaa  <  1:3238460/68‑1 (MQ=255)
                                                                  |                                                            
AGCCCCATCAGGTCGCGTTGACGAATATGTTTTTGAATTAACTCCAGCAGCGCCATACGTCGGTGCTGCATGATTTCATCATCAGGCATGACGGTGACATCAATCAGCGGAAATGCGGAGGCATAAA  >  minE/2677358‑2677484

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