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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 385,938 G→C 17.6% C383S (TGT→TCT) ‡ cstA → carbon starvation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE385,9380GC17.6% 149.3 / 24.9 68C383S (TGT→TCT) ‡cstAcarbon starvation protein
Reads supporting (aligned to +/- strand):  ref base G (29/27);  new base C (7/5);  total (36/32)
Fisher's exact test for biased strand distribution p-value = 7.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.66e-01

TGCTTTATCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGACGGCG  >  minE/385871‑386008
                                                                   |                                                                      
tGCTTTATCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTat                                                                     <  1:475505/71‑1 (MQ=255)
  cTTTATCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTatc                                                                    >  1:1265994/1‑70 (MQ=255)
    tcaTCGGCTACGGCGCAATGCTGATGGAGTCCTTCGTGGCGATTATGGCGCTGGTTGCTGCGTCCatcatc                                                                 >  1:1675089/3‑71 (MQ=255)
     tATCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTatcatc                                                                 >  1:2580016/1‑70 (MQ=255)
     tATCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTatcatc                                                                 >  1:1590061/1‑70 (MQ=255)
     caTCGGCTACGGCGCAATGCTGATGGAGTCCTTCGTGGCGATTATGGCGCTGGTTGCTGCGTCCatcatc                                                                 >  1:1201926/2‑70 (MQ=255)
     caTCGGCTACGGCGCAATGCTGATGGAGTCCTTCGTGGCGATTATGGCGCTGGTTGCTGCGTCCatcatc                                                                 <  1:2777135/69‑1 (MQ=255)
      aTCGGCTACGGCGCAATGCTGATGGAGTCCTTCGTGGCGATTATGGCGCTGGTTGCTGCGTCCATCATCGa                                                               <  1:1146750/71‑1 (MQ=255)
       tCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGa                                                               <  1:3352639/70‑1 (MQ=255)
       tCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGAt                                                              >  1:2968835/1‑71 (MQ=255)
       tCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTACGCCTGTATCATCGAt                                                              <  1:174871/71‑1 (MQ=255)
        cGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGAt                                                              <  1:1027440/70‑1 (MQ=255)
         ggCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATc                                                             <  1:2534966/70‑1 (MQ=255)
         ggCTACGGCGCAATGCTGATGGAGTCCTTCGTGGCGATTATGGCGCTGGTTGCTGCGTCCATCATCGAAcc                                                            <  1:1272316/71‑1 (MQ=255)
         ggCTACGGCGCAATGCTGATGGAGTCCTTCGTGGAGATTATGGCGCTGGTTGCTGCGTCCATCATCGaac                                                             >  1:3782389/1‑68 (MQ=255)
           cTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCgg                                                          >  1:1846836/1‑71 (MQ=255)
              cGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCg                                                       <  1:2697598/71‑1 (MQ=255)
                   ggATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCgg                                                          <  1:2117396/63‑1 (MQ=255)
                     aTGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTAttt                                                >  1:2733142/1‑71 (MQ=255)
                      tGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTa                                                                      >  1:324658/1‑48 (MQ=255)
                      tGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTAtttt                                               <  1:3409863/71‑1 (MQ=255)
                      tGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTCTCCGCCTGTATCATCGATcc                                                            >  1:743209/1‑58 (MQ=255)
                       gTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCggg                                                         <  1:1559909/60‑1 (MQ=255)
                       gTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTAttt                                                >  1:3677136/1‑69 (MQ=255)
                          aaTGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTAttt                                                >  1:617591/1‑66 (MQ=255)
                          aaTGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTAttt                                                <  1:1664047/66‑1 (MQ=255)
                          aaTGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGcc                                            >  1:406668/1‑70 (MQ=255)
                           aTGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCAt                                          >  1:2331529/1‑71 (MQ=255)
                            tGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGc                                                        >  1:2330920/1‑56 (MQ=255)
                            tGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATg                                         <  1:3649642/71‑1 (MQ=255)
                            tGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATg                                         <  1:1408146/71‑1 (MQ=255)
                                gtCCTTCGTGGCGATTATGGCGCTGGTTGCTGCGTCCATCATCGAACCGGGTCTTTACTTCGCGATGAACa                                     <  1:2450192/70‑1 (MQ=255)
                                aTCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATg                                         >  1:1329927/1‑67 (MQ=255)
                                aTCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGa                                        >  1:1494920/1‑68 (MQ=255)
                                aTCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACa                                     <  1:2018197/71‑1 (MQ=255)
                                 tCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGc                                                        >  1:3828925/1‑51 (MQ=255)
                                 tCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTg                                              <  1:2107254/61‑1 (MQ=255)
                                   cTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGcc                                  <  1:1425091/71‑1 (MQ=255)
                                   cTTCGTGGCGATTATGGCGCTGGTTGCTGCGTCCATCATCGAACCGGGTCTTTACTTCGCGATGAACac                                    >  1:2351686/1‑68 (MQ=255)
                                     tCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCgt                                                      >  1:3333672/1‑49 (MQ=255)
                                     tCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGccc                                 >  1:1677542/1‑70 (MQ=255)
                                      cGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGccc                                 <  1:3012109/69‑1 (MQ=255)
                                      cGTGGCGATTATGGCGCTGGTTGCTGCGTCCATCATCGAACCGGGTCTTTACTTCGCGATGAACACCCCgc                               >  1:3528104/1‑70 (MQ=255)
                                       gTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTAtt                                                 <  1:3694265/52‑1 (MQ=255)
                                       gTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATg                                         <  1:3506746/60‑1 (MQ=255)
                                              ttATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGt                        >  1:3021694/1‑70 (MQ=255)
                                              ttATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGt                        >  1:2256305/1‑70 (MQ=255)
                                              ttATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTg                       <  1:14396/71‑1 (MQ=255)
                                              ttATGGCGCTGGTTGCTGCGTCCATCATCGAACCGGGTCTTTACTTCGCGATGaa                                       >  1:1355696/1‑55 (MQ=255)
                                              ttATGGCGCTGGTTGCTGCGTCCATCATCGAACCGGGTCTTTACTTCGCGATGaa                                       >  1:3722328/1‑55 (MQ=255)
                                               tATGGCGCTGGTTGCTGCGTCCATCATCGAACCGGGTCTTTACTTCGCGATGAAc                                      <  1:2112680/55‑1 (MQ=255)
                                                aTGGCGCTGGTTTCCGCCTGTATCATCGATCCggg                                                         >  1:808085/1‑35 (MQ=255)
                                                aTGGCGCTGGTTTCCGCCTGTATCATCGATCCggg                                                         >  1:3884738/1‑35 (MQ=255)
                                                aTGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGa                                        <  1:1431758/52‑1 (MQ=255)
                                                 tGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGt                        <  1:2764697/67‑1 (MQ=255)
                                                    cgcTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAGCAGCCCGATGGCGGTGCTGGCt                 <  1:724819/71‑1 (MQ=255)
                                                    cgcTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCt                 <  1:449226/71‑1 (MQ=255)
                                                     gcTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTc                >  1:1405036/1‑71 (MQ=255)
                                                      cTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATg                                         <  1:110534/45‑1 (MQ=255)
                                                      cTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCAAGAACAGcc                                  >  1:2128327/1‑52 (MQ=255)
                                                         gTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCgg             <  1:3141410/70‑1 (MQ=255)
                                                            tCCGCCTGTATCATCGATCCGGGCGTGTATTTTGcc                                            >  1:1259441/1‑36 (MQ=255)
                                                             ccGCCTGTATCATCGATCCGGGCGTGTATTTTGcc                                            >  1:375767/1‑35 (MQ=255)
                                                             ccGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAgg         >  1:2988646/1‑70 (MQ=255)
                                                              cGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAggg        <  1:1597973/70‑1 (MQ=255)
                                                              cGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGa       >  1:3278000/1‑71 (MQ=255)
                                                              cGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGa       >  1:254284/1‑71 (MQ=255)
                                                                ccTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGAcg     <  1:285236/71‑1 (MQ=255)
                                                                   gTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGAcggcg  >  1:3698815/1‑71 (MQ=255)
                                                                   |                                                                      
TGCTTTATCGGCTACGGTGGGATGTTAATGGAATCCTTCGTGGCGATTATGGCGCTGGTTTCCGCCTGTATCATCGATCCGGGCGTGTATTTTGCCATGAACAGCCCGATGGCGGTGCTGGCTCCGGCAGGGACGGCG  >  minE/385871‑386008

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