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 2,028,614 A→G 21.6% P40P (CCT→CCC)  parC ← DNA topoisomerase IV, subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,028,6140AG21.6% 182.5 / 39.1 129P40P (CCT→CCC) parCDNA topoisomerase IV, subunit A
Reads supporting (aligned to +/- strand):  ref base A (34/67);  new base G (15/13);  total (49/80)
Fisher's exact test for biased strand distribution p-value = 7.75e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.08e-01

Only 100 of 131 total aligned reads displayed.

GATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATGGAGTAG  >  minE/2028546‑2028674
                                                                    |                                                            
gATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACa                                                              <  1:1343950/69‑1 (MQ=255)
                   tGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCaa                                           <  1:2417903/69‑1 (MQ=255)
                    ggCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCaa                                           <  1:971207/68‑1 (MQ=255)
                          cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCAt                                                 <  1:3376127/56‑1 (MQ=255)
                          cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCAt                                                 <  1:3221231/56‑1 (MQ=255)
                          cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCAt                                                 <  1:2519928/56‑1 (MQ=255)
                          cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACg                                     >  1:3308551/1‑68 (MQ=255)
                          cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACg                                     >  1:1126273/1‑68 (MQ=255)
                          cAGGCCCAGTTCAGACATCGCATACA‑AATGCGGCGCTGAACAGGTTTCAGACCAt                                                 <  1:2468136/55‑1 (MQ=255)
                            ggCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   <  1:872389/68‑1 (MQ=255)
                            ggCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   <  1:839278/68‑1 (MQ=255)
                            ggCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   <  1:1231912/68‑1 (MQ=255)
                            ggCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   <  1:2313620/68‑1 (MQ=255)
                            gccccAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   <  1:1880560/66‑1 (MQ=255)
                                     cAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACgg                          >  1:2394232/1‑68 (MQ=255)
                                     cAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACgg                          >  1:1355649/1‑68 (MQ=255)
                                          aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                             <  1:2132726/44‑1 (MQ=255)
                                          aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                             <  1:2104881/44‑1 (MQ=255)
                                          aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                             <  1:2397584/44‑1 (MQ=255)
                                          aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                             <  1:2893610/44‑1 (MQ=255)
                                          aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                             <  1:1840560/44‑1 (MQ=255)
                                          aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                             <  1:2301913/44‑1 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATaa                                        >  1:1120716/1‑46 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:2430533/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:2433741/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:90864/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:3066465/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:1822418/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:2387741/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:876834/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:2318503/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:2582595/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:2106320/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:1221571/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:2303769/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                                   >  1:2303688/1‑51 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATc                 >  1:1092388/1‑69 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATc                 >  1:885774/1‑69 (MQ=255)
                                             gCATACACAATGCGGCGCTGAACAGGTTTCAGACAATCACCAATAAACGGc                                   >  1:818066/1‑51 (MQ=255)
                                                  tccaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:338636/67‑1 (MQ=255)
                                                  tccaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:3379969/67‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCGACGCACGGTCCATGATCACGTa            <  1:706171/69‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGa                   >  1:698520/1‑62 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:2517076/69‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:1555527/69‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            >  1:652316/1‑69 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:2634602/69‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:2981076/69‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            >  1:3260987/1‑69 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:1026220/69‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:1105164/69‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            >  1:841762/1‑69 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            >  1:1252117/1‑69 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:1504761/69‑1 (MQ=255)
                                                  cacaATGCGGCGCTGAACAGGTTTCAAACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa            <  1:1095110/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1007228/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:3312190/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1625323/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:3031716/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:403197/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:45657/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1954308/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1247753/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:2212083/69‑1 (MQ=255)
                                                    caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:2237093/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:2778237/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:2859509/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1086792/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:2612034/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:621032/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1775505/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:543235/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:3139947/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1083781/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1504819/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:1533014/69‑1 (MQ=255)
                                                    caATGCGCCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:3095526/69‑1 (MQ=255)
                                                     aaTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:996045/68‑1 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:1016815/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:1163548/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:1182068/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:2698230/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:55981/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:1584574/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:2608177/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:2575203/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                       >  1:1760084/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCACAAATAAACGGCAACGCACGGTcc                       >  1:2376840/1‑55 (MQ=255)
                                                     aaTGCGCCGCTGAACGGGTTTCAGACCATCA‑CAATAAACGGCAACGCACGGTcc                       >  1:3360050/1‑54 (MQ=255)
                                                      aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg        <  1:2499361/69‑1 (MQ=255)
                                                      aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg        <  1:1189848/69‑1 (MQ=255)
                                                      aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg        <  1:1359734/69‑1 (MQ=255)
                                                      aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg        <  1:2041247/69‑1 (MQ=255)
                                                      aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg        <  1:263808/69‑1 (MQ=255)
                                                      aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg        <  1:2855394/69‑1 (MQ=255)
                                                      aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg        <  1:365165/69‑1 (MQ=255)
                                                      aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg        <  1:3223824/69‑1 (MQ=255)
                                                      aTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa          <  1:2227734/67‑1 (MQ=255)
                                                            cgcTGAACAGGATTCAGACCATCACCAATAAACGGc                                   <  1:3230025/36‑1 (MQ=255)
                                                             gcTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATGGagtag  >  1:606889/1‑68 (MQ=255)
                                                                    |                                                            
GATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATGGAGTAG  >  minE/2028546‑2028674

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