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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,274,778 G→A 84.6% S30N (AGC→AAC)  yodA → conserved metal‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,274,7780GA84.6% 239.5 / 31.8 104S30N (AGC→AAC) yodAconserved metal‑binding protein
Reads supporting (aligned to +/- strand):  ref base G (8/8);  new base A (45/43);  total (53/51)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

Only 100 of 104 total aligned reads displayed.

GCTGTTGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTACAAAACCGAAC  >  minE/1274710‑1274846
                                                                    |                                                                    
gCTGTTGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGc                                                                     <  1:5650727/70‑1 (MQ=255)
gCTGTTGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAAcc                                                                    >  1:1236216/1‑71 (MQ=255)
 cTGTTGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGc                                                                     <  1:4345753/69‑1 (MQ=255)
  tGTTGCTTTAGGTGTCTTTATTGTTAGCGATCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCt                                                                  >  1:3767591/1‑71 (MQ=255)
   gTTGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCt                                                                  >  1:1554569/1‑70 (MQ=255)
    ttGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGCCCtt                                                                 <  1:3439014/70‑1 (MQ=255)
    ttGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCtt                                                                 >  1:974804/1‑70 (MQ=255)
    ttGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCtt                                                                 <  1:1972305/70‑1 (MQ=255)
    ttGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCtt                                                                 <  1:2804191/70‑1 (MQ=255)
     tGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTaa                                                               >  1:3485196/1‑71 (MQ=255)
         ttAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGCCCTTAACa                                                             >  1:3817937/1‑69 (MQ=255)
         ttAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACa                                                             >  1:5664454/1‑69 (MQ=255)
         ttAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACa                                                             >  1:2621923/1‑69 (MQ=255)
          tAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACagag                                                          >  1:2625744/1‑71 (MQ=255)
              tgtCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCg                                                      <  1:2980073/71‑1 (MQ=255)
              tgtCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCg                                                      <  1:4953071/71‑1 (MQ=255)
              tgtCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCg                                                      <  1:2163624/71‑1 (MQ=255)
              tgtCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCg                                                      <  1:2157204/71‑1 (MQ=255)
                tCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACa                                                             >  1:2750315/1‑62 (MQ=255)
                tCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTc                                                       <  1:4787329/68‑1 (MQ=255)
                 cTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGaa                                                    >  1:2794863/1‑70 (MQ=255)
                  tttATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGCCCTTAACAGAGGTCGAAc                                                   >  1:3767266/1‑70 (MQ=255)
                  tttATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGCCCTTAACAGAGGTCGAAc                                                   >  1:3395401/1‑70 (MQ=255)
                  tttATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGa                                                     <  1:3804623/68‑1 (MQ=255)
                  tttATTGTTAGCACTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGa                                                     <  1:4856099/68‑1 (MQ=255)
                   ttATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACa                                                  >  1:5460103/1‑70 (MQ=255)
                    tATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACaa                                                 <  1:4823162/70‑1 (MQ=255)
                     aTTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACaaa                                                >  1:3853088/1‑70 (MQ=255)
                     aTTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACaaa                                                <  1:3156461/70‑1 (MQ=255)
                      ttGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACaaaaa                                              <  1:3091054/71‑1 (MQ=255)
                       tGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACa                                                             >  1:4519697/1‑55 (MQ=255)
                       tGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACa                                                             >  1:4737912/1‑55 (MQ=255)
                         ttAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgc                                            <  1:3788053/70‑1 (MQ=255)
                           aGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGaa                                                    >  1:3656174/1‑60 (MQ=255)
                            gcgcTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:5651844/71‑1 (MQ=255)
                            gcgcTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAg                                             >  1:5679512/1‑66 (MQ=255)
                              gcTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:1204898/69‑1 (MQ=255)
                              gcTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:873687/69‑1 (MQ=255)
                               cTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGCCCTTAACAGAGGTCGAACaa                                                 <  1:602846/59‑1 (MQ=255)
                               cTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:2969267/68‑1 (MQ=255)
                               cTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:258564/68‑1 (MQ=255)
                               cTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:5007752/68‑1 (MQ=255)
                               cTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:5278469/68‑1 (MQ=255)
                               cTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:4125583/68‑1 (MQ=255)
                               cTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTaa                                      >  1:3921609/1‑70 (MQ=255)
                                 ccTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACagag                                                          >  1:123460/1‑48 (MQ=255)
                                 ccTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTaa                                      >  1:1840592/1‑68 (MQ=255)
                                  cTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTa                                       <  1:521916/66‑1 (MQ=255)
                                  cTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTa                                       <  1:4223312/66‑1 (MQ=255)
                                  cTGCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATg                                    <  1:1876065/69‑1 (MQ=255)
                                    gCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGgtgt                                >  1:842089/1‑71 (MQ=255)
                                    gCCTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGgt                                  >  1:3768572/1‑69 (MQ=255)
                                     ccTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGtt                               >  1:1993059/1‑71 (MQ=255)
                                     ccTTTTCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGtt                               >  1:1787575/1‑71 (MQ=255)
                                         ttCGCATGGTCATCACTCACACGGCAAGCCCTTAACagag                                                          >  1:909722/1‑40 (MQ=255)
                                         ttCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgc                                         >  1:1145817/1‑57 (MQ=255)
                                         ttCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGttttt                            >  1:1896652/1‑70 (MQ=255)
                                         ttCGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGttttt                            >  1:1758066/1‑70 (MQ=255)
                                           cGCATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTtga                          <  1:448512/70‑1 (MQ=255)
                                            gCATGGTCATCACTCACACGGCAAGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTtgat                         >  1:3872552/1‑70 (MQ=255)
                                             cATGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTtgat                         <  1:3123832/69‑1 (MQ=255)
                                              aTGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgct                                           <  1:1669618/50‑1 (MQ=255)
                                               tGGTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACaaaaa                                              <  1:2874960/46‑1 (MQ=255)
                                                ggTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACaaa                                                <  1:1353013/43‑1 (MQ=255)
                                                 gTCATCACTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAg                                             >  1:3783436/1‑45 (MQ=255)
                                                  tcatcaCTCACACGGCAAGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCa                  <  1:1092959/71‑1 (MQ=255)
                                                  tcatcaCTCACACGGCAAGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCa                  <  1:5283905/71‑1 (MQ=255)
                                                  tcatcaCTCACACGGCAAGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCa                  <  1:4850642/71‑1 (MQ=255)
                                                  tcatcaCTCACACGGCAAACCCTTAACAGAGGTCGAACaaaaa                                              <  1:615119/43‑1 (MQ=255)
                                                    atcaCTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgc                                            >  1:61163/1‑43 (MQ=255)
                                                    atcaCTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgc                                            >  1:11948/1‑43 (MQ=255)
                                                    atcaCTCACACGGCAAACCCTTAACAGAGGTCGAACAAAAAgc                                            >  1:961634/1‑43 (MQ=255)
                                                     tcactcacACGGCAAACCCTTAACAGAGGTCGAACaaa                                                <  1:640487/38‑1 (MQ=255)
                                                      cactcacACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGgtgt                                >  1:1975232/1‑53 (MQ=255)
                                                       actcacACGGCAAGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTtgat                         >  1:4180980/1‑59 (MQ=255)
                                                       actcacACGGCAAACCCTTAACAGAGGTCGAACaaaa                                               >  1:575952/1‑37 (MQ=255)
                                                       actcacACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGcc                   >  1:1797966/1‑65 (MQ=255)
                                                       actcacACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTa             >  1:3628827/1‑71 (MQ=255)
                                                        ctcacACGGCAAACCCTTAACAGAGGTCGAACaaaaa                                              <  1:499617/37‑1 (MQ=255)
                                                        ctcacACGGCAAACCCTTAACAGAGGTCGAACaaaaa                                              <  1:3519648/37‑1 (MQ=255)
                                                        ctcacACGGCAAACCCTTAACAGAGGTCGAACaaaaa                                              <  1:5629144/37‑1 (MQ=255)
                                                        ctcacACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTAc            <  1:3605709/71‑1 (MQ=255)
                                                        ctcacACGGCAAACCCTTAAAAGAGGTCGAACaaaaa                                              <  1:128345/37‑1 (MQ=255)
                                                         tcacACGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGttt                              <  1:3376443/52‑1 (MQ=255)
                                                          cacaCGGCAAACCCTTAACAGAGGTCGAACAAAAAgc                                            >  1:233857/1‑37 (MQ=255)
                                                          cacaCGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTgatgat                      <  1:3813044/59‑1 (MQ=255)
                                                           acacGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgc                                         >  1:2155526/1‑39 (MQ=255)
                                                           acacGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTtga                          >  1:2235897/1‑54 (MQ=255)
                                                           acacGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTACaa          >  1:4116738/1‑70 (MQ=255)
                                                           acacGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTACaa          >  1:5432600/1‑70 (MQ=255)
                                                           acacGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTACaa          <  1:3193942/70‑1 (MQ=255)
                                                             acGGCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTtga                          >  1:1320633/1‑52 (MQ=255)
                                                              cGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:3935503/37‑1 (MQ=255)
                                                              cGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:3105090/37‑1 (MQ=255)
                                                              cGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:1873301/37‑1 (MQ=255)
                                                              cGGCAAACCCTTAACAGAGGTCGAACAAAAAgctgct                                        <  1:211026/37‑1 (MQ=255)
                                                               ggCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTACAAAAcc      >  1:4492397/1‑70 (MQ=255)
                                                                gCAAACCCTTAACAGAGGTCGAACAAAAAGCTGCTaa                                      >  1:5305633/1‑37 (MQ=255)
                                                                  aaGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTACAAAACCGAAc  >  1:2766607/1‑71 (MQ=255)
                                                                   aGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTtg                           >  1:5549558/1‑45 (MQ=255)
                                                                    |                                                                    
GCTGTTGCTTTAGGTGTCTTTATTGTTAGCGCTCCTGCCTTTTCGCATGGTCATCACTCACACGGCAAGCCCTTAACAGAGGTCGAACAAAAAGCTGCTAATGGTGTTTTTGATGATGCCAATGTACAAAACCGAAC  >  minE/1274710‑1274846

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