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 2,949,119 T→C 41.5% T10T (ACA→ACG)  yjjP ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,949,1190TC41.5% 29.4 / 64.7 89T10T (ACA→ACG) yjjPpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (28/24);  new base C (16/21);  total (44/45)
Fisher's exact test for biased strand distribution p-value = 3.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.95e-01

CAACCAACGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTG  >  minE/2949058‑2949182
                                                             |                                                               
caaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACgg                                                          >  1:2861932/1‑69 (MQ=255)
caaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACgg                                                          >  1:288381/1‑69 (MQ=255)
caaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACgg                                                          >  1:1470506/1‑69 (MQ=255)
caaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACgg                                                          >  1:1149332/1‑69 (MQ=255)
caaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACgg                                                          >  1:1164545/1‑69 (MQ=255)
caaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACgg                                                          >  1:571538/1‑69 (MQ=255)
caaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACgg                                                          >  1:1260973/1‑69 (MQ=255)
caaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACg                                                           >  1:1271185/1‑68 (MQ=255)
 aaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGc                                                         >  1:2327095/1‑69 (MQ=255)
 aaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGc                                                         >  1:2472352/1‑69 (MQ=255)
 aaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGc                                                         >  1:1688820/1‑69 (MQ=255)
 aaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGc                                                         >  1:1167741/1‑69 (MQ=255)
 aaccaacGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGc                                                         >  1:1216292/1‑69 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:1092477/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:1893243/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:1019298/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:2659048/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:951176/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:1042135/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:159725/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:1555390/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:1487994/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:425564/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTg                                       <  1:824271/69‑1 (MQ=255)
                   aCCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCCCAGTTTg                                       <  1:933712/69‑1 (MQ=255)
                        gTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATaa                                  <  1:1424899/69‑1 (MQ=255)
                        gTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATaa                                  <  1:1883652/69‑1 (MQ=255)
                        gTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATaa                                  <  1:239417/69‑1 (MQ=255)
                          tGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAAc                                 >  1:2488465/1‑68 (MQ=255)
                          tGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACt                                >  1:342779/1‑69 (MQ=255)
                          tGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACt                                >  1:3136799/1‑69 (MQ=255)
                          tGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACt                                >  1:44300/1‑69 (MQ=255)
                          tGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACt                                >  1:997825/1‑69 (MQ=255)
                          tGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACt                                >  1:1269031/1‑69 (MQ=255)
                          tGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACt                                >  1:1799653/1‑69 (MQ=255)
                                aGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCt                          >  1:2101133/1‑69 (MQ=255)
                                aGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCt                          >  1:383361/1‑69 (MQ=255)
                                aGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCt                          >  1:155775/1‑69 (MQ=255)
                                aGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCt                          >  1:1607354/1‑69 (MQ=255)
                                aGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCt                          >  1:2777184/1‑69 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:546514/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:1482264/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:754757/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:3426114/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:3369056/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:1568893/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:846161/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:2959611/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:873952/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:266014/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:1736909/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:2556372/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:899274/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:2451962/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:942791/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:239891/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:1896523/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:2259647/69‑1 (MQ=255)
                                  aaaTAATCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:1093032/69‑1 (MQ=255)
                                     taatCCACACTGGATACAAAGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGGCCttt                        <  1:803567/66‑1 (MQ=255)
                                         ccACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAg                 <  1:1960001/69‑1 (MQ=255)
                                         ccACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAg                 <  1:661993/69‑1 (MQ=255)
                                          cacaCTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGa                <  1:900817/69‑1 (MQ=255)
                                                     cAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCa                    >  1:1998726/1‑54 (MQ=255)
                                                     cAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCa                    >  1:757281/1‑54 (MQ=255)
                                                     cAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCa                    >  1:915482/1‑54 (MQ=255)
                                                     cAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTa     <  1:447318/69‑1 (MQ=255)
                                                     cAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTa     <  1:102553/69‑1 (MQ=255)
                                                     cAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTa     <  1:1295023/69‑1 (MQ=255)
                                                     cAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTa     <  1:717794/69‑1 (MQ=255)
                                                     cAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTa     <  1:3419075/69‑1 (MQ=255)
                                                      aaaGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCttt                        <  1:1583771/49‑1 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATaa                                  >  1:538276/1‑37 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATa                  >  1:1028422/1‑53 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTAtt   >  1:480926/1‑68 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTAtt   >  1:276296/1‑68 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTAtt   >  1:1147254/1‑68 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTAtt   >  1:3342034/1‑68 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTg  >  1:3122027/1‑69 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTg  >  1:862261/1‑69 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTg  >  1:789209/1‑69 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTg  >  1:2757494/1‑69 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTg  >  1:1802374/1‑69 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTg  >  1:2063408/1‑69 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTg  >  1:990972/1‑69 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTg  >  1:584304/1‑69 (MQ=255)
                                                        aGCCGCGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCG‑CCTTTGTCATAGACGTGCTGCGTATTg  >  1:1989428/1‑68 (MQ=255)
                                                        aGCCGCGTTACCGCTCGCTGTTGCTCAGTTTGCATAACTCGc                             >  1:381205/1‑42 (MQ=38)
                                                         gCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATaa                                  <  1:63173/36‑1 (MQ=255)
                                                             tgtTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTa     <  1:890885/61‑1 (MQ=255)
                                                             |                                                               
CAACCAACGCGCTTTCCGCACCATGTTGCAAAAGAAATAATCCACACTGGATACAAAGCCGTGTTACGGCTCGCTGTTGCTCAGTTTGCATAACTCGCCCTTTGTCATAGACGTGCTGCGTATTG  >  minE/2949058‑2949182

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