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 2,278,398 G→A 28.5% S117S (AGC→AGT)  btuB ← vitamin B12/cobalamin outer membrane transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,278,3980GA28.5% 85.1 / 32.0 82S117S (AGC→AGT) btuBvitamin B12/cobalamin outer membrane transporter
Reads supporting (aligned to +/- strand):  ref base G (42/15);  new base A (17/6);  total (61/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACACCAACA  >  minE/2278332‑2278462
                                                                  |                                                                
aCCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTgg                                                                  >  1:1709006/1‑67 (MQ=255)
aCCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTgg                                                                  >  1:540276/1‑67 (MQ=255)
aCCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTgg                                                                  >  1:1720678/1‑67 (MQ=255)
aCCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTgg                                                                  >  1:2997431/1‑67 (MQ=255)
aCCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTgg                                                                  >  1:2879070/1‑67 (MQ=255)
aCCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTgg                                                                  >  1:3224479/1‑67 (MQ=255)
aCCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTgg                                                                  >  1:2985009/1‑67 (MQ=255)
aCCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTgg                                                                  >  1:1882917/1‑67 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGTAACTGGCTAAg                                                             >  1:512236/1‑69 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTaa                                                              >  1:3429119/1‑68 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAg                                                             <  1:1227456/69‑1 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAg                                                             >  1:2893434/1‑69 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAg                                                             >  1:2796826/1‑69 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAg                                                             >  1:149357/1‑69 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAg                                                             >  1:3048992/1‑69 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAg                                                             >  1:2189815/1‑69 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAg                                                             >  1:742327/1‑69 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAg                                                             >  1:1720340/1‑69 (MQ=255)
   aTAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAACCGCAATAGGGAACTGGCTAAg                                                             >  1:1820072/1‑69 (MQ=255)
        cAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCgg                                                        <  1:1899446/69‑1 (MQ=255)
        cAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCgg                                                        <  1:3427642/69‑1 (MQ=255)
        cAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCgg                                                        <  1:1413371/69‑1 (MQ=255)
           cGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAg                                                     <  1:1596690/69‑1 (MQ=255)
           cGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAg                                                     <  1:749399/69‑1 (MQ=255)
                cgcgGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCa                                                <  1:561699/69‑1 (MQ=255)
                cgcgGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCa                                                <  1:1161841/69‑1 (MQ=255)
                cgcgGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCa                                                <  1:2923044/69‑1 (MQ=255)
                cgcgGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCa                                                <  1:1904169/69‑1 (MQ=255)
                cgcgGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCa                                                <  1:1268772/69‑1 (MQ=255)
                 gcgGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCa                                                <  1:1611373/68‑1 (MQ=255)
                             tatatTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTATGGTCgg                                                        <  1:557064/48‑1 (MQ=255)
                                     acacGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAGAACCa                                                <  1:1129110/48‑1 (MQ=255)
                                     acacGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAGAACCa                                                <  1:2612304/48‑1 (MQ=255)
                                       acGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCg                         <  1:1681071/69‑1 (MQ=255)
                                       acGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCg                         <  1:89359/69‑1 (MQ=255)
                                       acGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCg                         <  1:709851/69‑1 (MQ=255)
                                        cGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCg                         <  1:1756036/68‑1 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:1697370/1‑69 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:2340097/1‑69 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:267662/1‑69 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:2450457/1‑69 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:3351368/1‑69 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:3263562/1‑69 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:1905095/1‑69 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:575522/1‑69 (MQ=255)
                                          cTGGACAAGCGCAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGAc                      >  1:3236452/1‑69 (MQ=255)
                                                   cgcAATAGGGAACTGTCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCaa              >  1:1126375/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCaa              >  1:2746433/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCaa              >  1:962531/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCaa              >  1:2484857/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCaa              >  1:1087193/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGCCTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGACGCCAt                 >  1:3236659/1‑65 (MQ=255)
                                                   cgcAATAGGGAACTGACTAAGATCAGCAGAACCACt                                              >  1:196886/1‑36 (MQ=25)
                                                   cgcAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGACGCCATCaa              >  1:41625/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGACGCCATCaa              >  1:1732736/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGACGCCATCaa              >  1:1778857/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGACGCCATCaa              >  1:1878934/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGACGCCATCaa              >  1:1908508/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGACGCCATCaa              >  1:2387653/1‑68 (MQ=255)
                                                   cgcAATAGGGAACTGACTAAGATCAGCAGAACCACTCACCCCCGCCAAATTCAGGCGGACGCCATCaa              >  1:2509478/1‑68 (MQ=255)
                                                      aaTAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTaa          <  1:2267532/69‑1 (MQ=255)
                                                          gtgAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:1396892/3‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGc                    >  1:2449884/1‑55 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCaaat            >  1:1933855/1‑61 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAAtt            >  1:1196357/1‑63 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAAtt            >  1:765186/1‑63 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAAtt            >  1:2439129/1‑63 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAAtt            >  1:3034357/1‑63 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAAtt            >  1:1874111/1‑63 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAAtt            >  1:1941097/1‑63 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAAtt            >  1:2690333/1‑63 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAacac       >  1:3087180/1‑68 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAaca        >  1:1147402/1‑67 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:660882/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:2308404/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:312474/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:3072583/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:2625955/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:2281550/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:227042/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:2176952/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:1899359/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:1692203/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:1655858/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:1475264/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:145630/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:1427925/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:1117434/1‑69 (MQ=255)
                                                          gggAACTGGCTAAGGTCGGCAGAACCACTCACCACCGCCAGATTCAGGCGTACGCCATCAATTAACAcc      >  1:727746/1‑69 (MQ=255)
                                                              aCTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACACCAaca  <  1:1625952/69‑1 (MQ=255)
                                                                  |                                                                
ACCATAAACAGCGGAGCGCGGCCCACGGATATATTCAACACGCTGGACAAGCGCAATAGGGAACTGGCTAAGGTCGGCAGAACCACTCACCCCCGCCAGATTCAGGCGTACGCCATCAATTAACACCAACA  >  minE/2278332‑2278462

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