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 2,028,605 G→C 22.3% R43R (CGC→CGG)  parC ← DNA topoisomerase IV, subunit A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,028,6050GC22.3% 227.8 / 60.4 130R43R (CGC→CGG) parCDNA topoisomerase IV, subunit A
Reads supporting (aligned to +/- strand):  ref base G (33/68);  new base C (15/14);  total (48/82)
Fisher's exact test for biased strand distribution p-value = 8.07e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 136 total aligned reads displayed.

ACGGGCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATG  >  minE/2028539‑2028668
                                                                  |                                                               
aCGGGCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATgcggcg                                                               >  1:856376/1‑69 (MQ=255)
aCGGGCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATgcggcg                                                               >  1:531931/1‑69 (MQ=255)
aCGGGCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATgcggcg                                                               >  1:495909/1‑69 (MQ=255)
aCGGGCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATgcggcg                                                               >  1:2857346/1‑69 (MQ=255)
   ggCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTg                                                            <  1:3205075/69‑1 (MQ=255)
       gATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACa                                                        <  1:1213098/69‑1 (MQ=255)
          tttttAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATgcggc                                                                >  1:1378000/1‑58 (MQ=255)
                           ggCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCaa                                     <  1:971207/68‑1 (MQ=255)
                                 cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCAt                                           <  1:1878415/56‑1 (MQ=255)
                                 cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCAt                                           <  1:3221231/56‑1 (MQ=255)
                                 cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCAt                                           <  1:2519928/56‑1 (MQ=255)
                                 cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACg                               >  1:2544898/1‑68 (MQ=255)
                                 cAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACg                               >  1:2633868/1‑68 (MQ=255)
                                 cAGGCCCAGTTCAGACATCGCATACA‑AATGCGGCGCTGAACAGGTTTCAGACCAt                                           <  1:2468136/55‑1 (MQ=255)
                                   ggCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             <  1:2313620/68‑1 (MQ=255)
                                   gccccAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             <  1:1880560/66‑1 (MQ=255)
                                            cAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACgg                    >  1:1355649/1‑68 (MQ=255)
                                            cAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACgg                    >  1:2394232/1‑68 (MQ=255)
                                            cAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACgg                    >  1:889724/1‑68 (MQ=255)
                                            cAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACgg                    >  1:3375931/1‑68 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:1695098/44‑1 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:2132726/44‑1 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:2104881/44‑1 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:2397584/44‑1 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:1840560/44‑1 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:809068/44‑1 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:1086444/44‑1 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:2301913/44‑1 (MQ=255)
                                                 aTCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCAcc                                       <  1:2893610/44‑1 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATaa                                  >  1:1120716/1‑46 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAAc                                >  1:2388128/1‑48 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             >  1:1221571/1‑51 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             >  1:2318503/1‑51 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             >  1:2303688/1‑51 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             >  1:2303769/1‑51 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             >  1:2430533/1‑51 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             >  1:3066465/1‑51 (MQ=255)
                                                    gCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGc                             >  1:876834/1‑51 (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)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      <  1:1105164/69‑1 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      <  1:2881161/69‑1 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      >  1:1252117/1‑69 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      <  1:2981076/69‑1 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      <  1:1504761/69‑1 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      >  1:645493/1‑69 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      >  1:652316/1‑69 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      <  1:1555527/69‑1 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      <  1:2468701/69‑1 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      >  1:3260987/1‑69 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      <  1:2417995/69‑1 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      >  1:841762/1‑69 (MQ=255)
                                                         cacaATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTa      <  1:1026220/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:2237093/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:3429433/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:403197/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:1146290/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:3034255/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:3312190/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:1247753/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:1007228/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:45657/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:1279349/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:2057811/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:2212083/69‑1 (MQ=255)
                                                           caATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:2245144/69‑1 (MQ=255)
                                                           caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:543235/69‑1 (MQ=255)
                                                           caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:1504819/69‑1 (MQ=255)
                                                           caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:2612034/69‑1 (MQ=255)
                                                           caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:1533014/69‑1 (MQ=255)
                                                           caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:1086792/69‑1 (MQ=255)
                                                           caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:842295/69‑1 (MQ=255)
                                                           caATGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:1775505/69‑1 (MQ=255)
                                                           caATGCGCCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:3095526/69‑1 (MQ=255)
                                                            aaTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACa    <  1:996045/68‑1 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:1016815/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:1100415/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:1163548/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:2698230/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:1182068/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:55981/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:2608177/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:2575203/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:2169903/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:1760084/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTcc                 >  1:1584574/1‑55 (MQ=255)
                                                            aaTGCGCCGCTGAACGGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTc                  >  1:3199105/1‑54 (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  <  1:1359734/69‑1 (MQ=255)
                                                             aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg  <  1:2041247/69‑1 (MQ=255)
                                                             aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg  <  1:263808/69‑1 (MQ=255)
                                                             aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg  <  1:2741260/69‑1 (MQ=255)
                                                             aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg  <  1:2855394/69‑1 (MQ=255)
                                                             aTGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATg  <  1:3282126/69‑1 (MQ=255)
                                                                  |                                                               
ACGGGCCGATTTTTTAAATTTGGCGCTGGCATTCAGGCCCAGTTCAGACATCGCATACACAATGCGGCGCTGAACAGGTTTCAGACCATCACCAATAAACGGCAACGCACGGTCCATGATCACGTACATG  >  minE/2028539‑2028668

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