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 1,831,056 T→C 25.1% intergenic (‑127/‑39) ygbI ← / → ygbJ predicted DNA‑binding transcriptional regulator/predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,831,0560TC25.1% 172.0 / 56.2 147intergenic (‑127/‑39)ygbI/ygbJpredicted DNA‑binding transcriptional regulator/predicted dehydrogenase, with NAD(P)‑binding Rossmann‑fold domain
Reads supporting (aligned to +/- strand):  ref base T (50/60);  new base C (26/11);  total (76/71)
Fisher's exact test for biased strand distribution p-value = 1.29e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.04e-02

Only 100 of 147 total aligned reads displayed.

ATGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTC  >  minE/1830997‑1831121
                                                           |                                                                 
aTGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATcaaacaa                                                          <  1:1086275/69‑1 (MQ=255)
   ttAATTTATGTGATTCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACaaaa                                                        >  1:1464250/1‑68 (MQ=255)
   ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACaaaa                                                        >  1:510619/1‑68 (MQ=255)
   ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                                                       >  1:1719606/1‑69 (MQ=255)
   ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                                                       <  1:2878562/69‑1 (MQ=255)
   ttAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                                                       <  1:1660879/69‑1 (MQ=255)
       tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                                                    <  1:2658823/68‑1 (MQ=255)
       tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                                                    <  1:1190144/68‑1 (MQ=255)
       tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                                                    <  1:2408791/68‑1 (MQ=255)
       tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                                                    <  1:2051324/68‑1 (MQ=255)
       tttATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATc                                                    <  1:1413835/68‑1 (MQ=255)
        ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                                                   <  1:1971586/65‑1 (MQ=255)
        ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                                                   <  1:2906717/65‑1 (MQ=255)
        ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                                                   <  1:2951066/65‑1 (MQ=255)
        ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                                                   <  1:3012459/65‑1 (MQ=255)
        ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                                                   <  1:462841/65‑1 (MQ=255)
        ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                                                   <  1:1500003/65‑1 (MQ=255)
        ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                                                   <  1:2247509/65‑1 (MQ=255)
        ttttgtgAATCAGCTCACCATATCGTTATCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCa                                                   <  1:1087442/65‑1 (MQ=255)
                       cACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAg                                     >  1:2836933/1‑67 (MQ=255)
                       cACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAg                                     >  1:2157790/1‑67 (MQ=255)
                       cACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAg                                     >  1:2923825/1‑67 (MQ=255)
                          cATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGagag                                <  1:765359/69‑1 (MQ=255)
                             aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             <  1:2185173/69‑1 (MQ=255)
                             aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             <  1:2220560/69‑1 (MQ=255)
                             aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             <  1:2373285/69‑1 (MQ=255)
                             aCCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             <  1:1042726/69‑1 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAat                                                       >  1:2079388/1‑42 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:2170759/1‑68 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:2367299/1‑68 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             <  1:2258108/68‑1 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:2971143/1‑68 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:3341260/1‑68 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:341168/1‑68 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:2422156/1‑68 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:1372247/1‑68 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:256822/1‑68 (MQ=255)
                              ccGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAg                             >  1:1147332/1‑68 (MQ=255)
                                  tATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaa                        <  1:3410014/69‑1 (MQ=255)
                                  tATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaa                        <  1:485577/69‑1 (MQ=255)
                                  tATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaa                        <  1:585218/69‑1 (MQ=255)
                                  tATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaa                        <  1:2810711/69‑1 (MQ=255)
                                  tATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaa                        <  1:2696041/69‑1 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTa                                               >  1:3058046/1‑45 (MQ=38)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGa                            >  1:2254534/1‑64 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATg                          >  1:197595/1‑66 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:2507601/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:958591/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:279164/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:3064547/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:531970/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:682511/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:933086/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:2441234/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1765201/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1792964/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1688439/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1581602/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:2203540/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1311185/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:2388587/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1231684/1‑69 (MQ=255)
                                   aTCTTTCCGCGCTTATATTCACAACATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:2492419/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:631766/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:123392/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:380443/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:3431058/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:848608/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:3284355/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:324362/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1005983/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1719952/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:2282404/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:2708709/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:2602310/1‑69 (MQ=255)
                                   aTCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaaa                       >  1:1779261/1‑69 (MQ=255)
                                     cTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGaa                        <  1:2075551/66‑1 (MQ=255)
                                      ttCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAAc                     >  1:3165219/1‑68 (MQ=255)
                                          aGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACggg                  <  1:2157784/67‑1 (MQ=255)
                                          aGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACggg                  <  1:465044/67‑1 (MQ=255)
                                          aGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACggg                  <  1:139151/67‑1 (MQ=255)
                                             gcTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTg             <  1:1675769/69‑1 (MQ=255)
                                             gcTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTg             <  1:1474197/69‑1 (MQ=255)
                                              cTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGa            >  1:1689268/1‑69 (MQ=255)
                                              cTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGa            >  1:3165016/1‑69 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:875390/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:1016067/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:1546888/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:779720/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:2388956/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:2793983/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:474721/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:1872646/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:3320966/68‑1 (MQ=255)
                                                   atTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:1778088/68‑1 (MQ=255)
                                                    ttCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCa      <  1:669917/69‑1 (MQ=255)
                                                    ttCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCa      <  1:1743724/69‑1 (MQ=255)
                                                    ttCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCa      <  1:2581974/69‑1 (MQ=255)
                                                      cacaATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGttt        <  1:542614/65‑1 (MQ=255)
                                                         aaTATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTc  <  1:2872079/68‑1 (MQ=255)
                                                           |                                                                 
ATGTTAATTTATGTGAATCAGATCACCATACCGTTATCTTCCAGCGCTTATATTCACAATATCAAACAAAATATCACTTAAATTAACAAGGAGAGCAGATGAAAACGGGATCTGAGTTTCATGTC  >  minE/1830997‑1831121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A