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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,211,683 A→G 37.9% I465I (ATT→ATC)  rng ← ribonuclease G

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,211,6830AG37.9% 69.2 / 99.1 87I465I (ATT→ATC) rngribonuclease G
Reads supporting (aligned to +/- strand):  ref base A (23/31);  new base G (23/10);  total (46/41)
Fisher's exact test for biased strand distribution p-value = 1.63e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACGACGTCAAACTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCGGAGAAGCA  >  minE/2211617‑2211749
                                                                  |                                                                  
tACGACGTCAAACTGCTCCTTGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACTAAGAttt                                                                >  1:4028738/1‑71 (MQ=255)
 acgacgTCAAACTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAGATTTc                                                               >  1:2303815/1‑71 (MQ=255)
 acgacgTCAAACTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAGATTTc                                                               >  1:412852/1‑71 (MQ=255)
  cgacgTCAAACTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTcc                                                              <  1:2550697/71‑1 (MQ=255)
  cgacgTCAAACTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTcc                                                              <  1:2484397/71‑1 (MQ=255)
  cgacgTCAAACTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTcc                                                              <  1:1846197/71‑1 (MQ=255)
         aaaCTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTcc                                                        >  1:44863/1‑70 (MQ=255)
         aaaCTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCg                                                       >  1:237404/1‑71 (MQ=255)
         aaaCTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCg                                                       >  1:588588/1‑71 (MQ=255)
              gCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAGATTTCCAc                                                            >  1:937878/1‑61 (MQ=255)
               cTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCg                                                 <  1:921102/71‑1 (MQ=255)
               cTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCg                                                 <  1:2160168/71‑1 (MQ=255)
               cTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCg                                                 <  1:2081124/71‑1 (MQ=255)
                 ccTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAg                                               >  1:2947580/1‑71 (MQ=255)
                      ttATAGAGCGGTTCAATTTGTTCTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAg                                                   <  1:1577070/62‑1 (MQ=255)
                      ttATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGa                                          <  1:1638839/71‑1 (MQ=255)
                       tataGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGAc                                         >  1:1256046/1‑71 (MQ=255)
                        ataGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGAc                                         <  1:1524310/70‑1 (MQ=255)
                        ataGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGAc                                         <  1:4255069/70‑1 (MQ=255)
                        ataGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGAc                                         <  1:2316557/70‑1 (MQ=255)
                           gagCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGActct                                      <  1:3027287/70‑1 (MQ=255)
                           gagCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTACACTTCCGCCAGCGAGTGTGActct                                      <  1:2732790/70‑1 (MQ=255)
                                gTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAAt                                                                  <  1:3537620/37‑1 (MQ=255)
                                gTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAAt                                                                  <  1:3044583/37‑1 (MQ=255)
                                gTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAAt                                                                  <  1:738234/37‑1 (MQ=255)
                                gTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCtt                                     <  1:3197020/66‑1 (MQ=255)
                                gTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCtt                                     <  1:55689/66‑1 (MQ=255)
                                 ttCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTcc                                                              <  1:1759574/40‑1 (MQ=255)
                                  tCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTcc                                                              <  1:1304864/39‑1 (MQ=255)
                                     aTTTGTACTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCaa                           <  1:3547930/71‑1 (MQ=255)
                                       ttGTACTTTAACCTGTTTGCCAACGAAAATTTCCa                                                             >  1:1376140/1‑35 (MQ=255)
                                       ttGTACTTTAACCTGTTTGCCAACGAAAATTTCCa                                                             >  1:2004230/1‑35 (MQ=255)
                                       ttGTACTTTAACCTGTTTGCCAACGAAAATTTCCa                                                             >  1:793078/1‑35 (MQ=255)
                                       ttGTACTTTAACCTGTTTGCCAACGAAAATTTCCa                                                             >  1:2705271/1‑35 (MQ=255)
                                       ttGTACTTTAACCTGTTTGCCAACGAAAATTTCCa                                                             >  1:1717412/1‑35 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGc                        >  1:1416339/1‑71 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGc                        >  1:889611/1‑71 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCCTTCAAGGc                        >  1:528050/1‑71 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCg                                                       <  1:1226927/40‑1 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCg                                                       <  1:219216/40‑1 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCg                                                       <  1:1857441/40‑1 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCg                                                       <  1:299758/40‑1 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGc                        >  1:329000/1‑71 (MQ=255)
                                        tGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGc                        >  1:4247473/1‑71 (MQ=255)
                                         gTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGc                        <  1:104032/70‑1 (MQ=255)
                                         gTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGc                        <  1:2854943/70‑1 (MQ=255)
                                          tACTTTAACCTGTTTGCCAACTAAGATTTCCACTTCCGCCAGCGa                                                <  1:200902/45‑1 (MQ=38)
                                          tACTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGa                                                <  1:1495973/45‑1 (MQ=255)
                                           aCTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAgt                                              >  1:4093641/1‑46 (MQ=255)
                                           aCTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAgt                                              >  1:932777/1‑46 (MQ=255)
                                           aCTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAgt                                              >  1:1259544/1‑46 (MQ=255)
                                           aCTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAgt                                              >  1:226407/1‑46 (MQ=255)
                                           aCTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAgt                                              >  1:2551835/1‑46 (MQ=255)
                                           aCTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAgt                                              >  1:2746801/1‑46 (MQ=255)
                                            cTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAgt                                              >  1:3461527/1‑45 (MQ=255)
                                            cTTTAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTc                     <  1:767051/70‑1 (MQ=255)
                                             tttAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAg                   >  1:77946/1‑71 (MQ=255)
                                             tttAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAg                   >  1:3364772/1‑71 (MQ=255)
                                             tttAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAg                   >  1:3003051/1‑71 (MQ=255)
                                             tttAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAg                   >  1:2234687/1‑71 (MQ=255)
                                             tttAACCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAg                   >  1:4250240/1‑71 (MQ=255)
                                             tttAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTc                                    <  1:3129447/54‑1 (MQ=255)
                                             tttAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTc                                    <  1:1591064/54‑1 (MQ=255)
                                             tttAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTc                                    <  1:1961690/54‑1 (MQ=255)
                                              ttAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGGCTTTCAAGGCTTCAGc                  >  1:1172430/1‑71 (MQ=255)
                                                aaCCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCt                 <  1:3672452/70‑1 (MQ=255)
                                                 aCCTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCt                 <  1:924930/69‑1 (MQ=255)
                                                 aCCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTAc               <  1:2587549/71‑1 (MQ=255)
                                                 aCCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTAc               <  1:2980385/71‑1 (MQ=255)
                                                   cTGTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTg             >  1:1270652/1‑71 (MQ=255)
                                                     gTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAgtgt                                            >  1:3866256/1‑38 (MQ=255)
                                                     gTTTGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGcc           >  1:1549658/1‑71 (MQ=255)
                                                     gTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGc                        >  1:1992726/1‑58 (MQ=255)
                                                     gTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGc                        >  1:2897966/1‑58 (MQ=255)
                                                      tttGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCg          >  1:1946767/1‑71 (MQ=255)
                                                      tttGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCg          >  1:3825269/1‑71 (MQ=255)
                                                      tttGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCg          >  1:2673807/1‑71 (MQ=255)
                                                      attGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTc                                    <  1:3486062/44‑1 (MQ=255)
                                                       ttGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCg          >  1:2695418/1‑70 (MQ=255)
                                                       ttGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCg          >  1:3511010/1‑70 (MQ=255)
                                                        tGCCAACGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCg          >  1:1018461/1‑69 (MQ=255)
                                                        tGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCg          >  1:4185331/1‑69 (MQ=255)
                                                        tGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCg          >  1:2580444/1‑69 (MQ=255)
                                                          ccAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCGgag       <  1:3407244/70‑1 (MQ=255)
                                                             aCGAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTc                             <  1:1186267/45‑1 (MQ=255)
                                                              cGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCGGAGAAGCa  <  1:588247/71‑1 (MQ=255)
                                                               gAAGATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCGGAGAAGCa  >  1:74495/1‑70 (MQ=255)
                                                                  |                                                                  
TACGACGTCAAACTGCTCCTGGTTATAGAGCGGTTCAATTTGTACTTTAACCTGTTTGCCAACGAAAATTTCCACTTCCGCCAGCGAGTGTGACTCTTCGCCTTTCAAGGCTTCAGCTACTGCCGGAGAAGCA  >  minE/2211617‑2211749

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