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
A5 F1 I0 R2 201 99.6 7939938 96.9% 7693799 60.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,514 T→C 100% pseudogene (647/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,5140TC100.0% 356.9 / NA 104pseudogene (647/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (52/52);  total (52/52)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

Only 100 of 104 total aligned reads displayed.

AGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAA  >  W3110S.gb/3824446‑3824578
                                                                    |                                                                 
aGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCt                                                                 >  1:6698015/1‑71 (MQ=255)
aGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCt                                                                 >  1:4359238/1‑71 (MQ=255)
 gACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCtt                                                                <  1:1213288/71‑1 (MQ=255)
   cGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttg                                                               <  1:6747737/70‑1 (MQ=255)
    gggCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgtt                                                             >  1:1110333/1‑71 (MQ=255)
      gcgcATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTgg                                                           <  1:673933/71‑1 (MQ=255)
          atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCCCCTTGTTGGcgct                                                       <  1:487626/71‑1 (MQ=255)
          atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgct                                                       >  1:7109228/1‑71 (MQ=255)
          atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgct                                                       <  1:5040326/71‑1 (MQ=255)
          atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgct                                                       <  1:4182776/71‑1 (MQ=255)
           tcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgc                                                        <  1:177718/69‑3 (MQ=255)
             atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc                                                    >  1:7318860/1‑71 (MQ=255)
             atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc                                                    >  1:1710656/1‑71 (MQ=255)
              ttGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGcc                                                   >  1:4150552/1‑71 (MQ=255)
               tGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGc                                                          >  1:2415772/1‑63 (MQ=255)
               tGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGc                                                          >  1:6034327/1‑63 (MQ=255)
               tGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                  >  1:3264162/1‑71 (MQ=255)
               agAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGc                                                          >  1:4608067/2‑63 (MQ=255)
                gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                  <  1:2817902/70‑1 (MQ=255)
                gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                  <  1:3630182/70‑1 (MQ=255)
                gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGcc                                                   <  1:2511492/69‑1 (MQ=255)
                 aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                 <  1:413270/70‑1 (MQ=255)
                 aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                 <  1:7296067/70‑1 (MQ=255)
                 aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                 <  1:4150338/70‑1 (MQ=255)
                 aaGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa                                                <  1:6395146/71‑1 (MQ=255)
                  aGTGCAGGGGACGGGAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g                                              <  1:4604734/71‑1 (MQ=255)
                      cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgt                                                              >  1:7699293/1‑52 (MQ=255)
                      cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttg                                                               >  1:7595596/1‑51 (MQ=255)
                      cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCtt                                                                >  1:5844285/1‑50 (MQ=255)
                      cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgc                                                        <  1:1250607/58‑3 (MQ=255)
                      cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg                                           >  1:1947380/1‑70 (MQ=255)
                         gggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggg                                          <  1:7788002/68‑2 (MQ=255)
                            aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCtt                                                                <  1:264397/44‑1 (MQ=255)
                            aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcga                                     <  1:1829609/71‑1 (MQ=255)
                              ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgtt                                                             <  1:3515097/45‑1 (MQ=255)
                              ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgtt                                                             <  1:3449604/45‑1 (MQ=255)
                              ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                  >  1:2715558/1‑56 (MQ=255)
                              ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                  >  1:1426662/1‑56 (MQ=255)
                              ggCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc                                                  >  1:6864164/1‑56 (MQ=255)
                               gCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgtt                                                             <  1:3546132/44‑1 (MQ=255)
                               gCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCttgtt                                                             <  1:107587/44‑1 (MQ=255)
                                cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTgg                                                           >  1:5832145/1‑45 (MQ=255)
                                 aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCa                                <  1:874521/71‑1 (MQ=255)
                                 aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g                                              >  1:4164726/1‑56 (MQ=255)
                                    aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg                             >  1:2139122/1‑71 (MQ=255)
                                     ggCGAGCCGTTCACCCTTGAAGAGCTACTCACCTTGTTGGc                                                          >  1:365220/1‑41 (MQ=38)
                                     ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGc                                                          >  1:6707203/1‑41 (MQ=255)
                                     ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa                                    >  1:4936076/1‑63 (MQ=255)
                                     ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg                                           >  1:2317236/1‑55 (MQ=255)
                                     ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg                                           >  1:2707366/1‑55 (MQ=255)
                                     ggCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg                                           >  1:3953243/1‑55 (MQ=255)
                                      gCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                 <  1:1339147/49‑1 (MQ=255)
                                      gCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg                                                 <  1:261956/49‑1 (MQ=255)
                                       cGAGCCGTTCACCCATGAAGAGCTACTCACCttgtt                                                             >  1:4279978/1‑36 (MQ=255)
                                       cGAGCCGTTCACCCATGAAGAGCTACTCACCttgtt                                                             >  1:4318763/1‑36 (MQ=255)
                                       cGAGCCGTTCACCCATGAAGAGCTACTCACCttgtt                                                             >  1:253101/1‑36 (MQ=255)
                                        gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgct                                                       <  1:2215367/41‑1 (MQ=38)
                                          gCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa                       >  1:587410/1‑71 (MQ=255)
                                           ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGAc                      <  1:5469895/71‑1 (MQ=255)
                                           ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg                                           >  1:5145938/1‑49 (MQ=255)
                                           ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg                                           >  1:4413152/1‑49 (MQ=255)
                                            cGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACg                     <  1:434113/71‑1 (MQ=255)
                                             gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg                                      <  1:2184134/53‑1 (MQ=255)
                                             gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGc                    <  1:754001/71‑1 (MQ=255)
                                                cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  >  1:1133733/1‑70 (MQ=255)
                                                cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  <  1:118785/70‑1 (MQ=255)
                                                 aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  <  1:5987580/69‑1 (MQ=255)
                                                 aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  <  1:1362021/69‑1 (MQ=255)
                                                 aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  <  1:6390437/69‑1 (MQ=255)
                                                   ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACg                     <  1:2411538/64‑1 (MQ=255)
                                                   ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg              >  1:4978768/1‑71 (MQ=255)
                                                    cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  <  1:3828196/66‑1 (MQ=255)
                                                    cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  <  1:5028531/66‑1 (MQ=255)
                                                    cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  <  1:4405816/66‑1 (MQ=255)
                                                    cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc             >  1:1497411/1‑71 (MQ=255)
                                                     aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa                                                >  1:2885762/1‑35 (MQ=37)
                                                     aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcg            >  1:613779/1‑71 (MQ=255)
                                                       gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAtt                              <  1:5185575/51‑1 (MQ=255)
                                                        aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt                               >  1:925024/1‑49 (MQ=255)
                                                        aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg         <  1:1942244/71‑1 (MQ=255)
                                                        aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg         <  1:1932923/71‑1 (MQ=255)
                                                         agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa                                    >  1:4814406/1‑43 (MQ=25)
                                                         agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc        >  1:535655/1‑71 (MQ=255)
                                                         agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc        <  1:5166287/71‑1 (MQ=255)
                                                         agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc        <  1:477527/71‑1 (MQ=255)
                                                          gagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt       <  1:7861937/71‑1 (MQ=255)
                                                           agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg                                      <  1:3347950/39‑1 (MQ=25)
                                                           agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg                                      <  1:1156647/39‑1 (MQ=25)
                                                            gCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaatc                                  >  1:6919679/1‑42 (MQ=25)
                                                            gCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaatc                                  >  1:2011530/1‑42 (MQ=25)
                                                            gCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa                       >  1:3442749/1‑53 (MQ=255)
                                                             cTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCa                   >  1:2789926/1‑56 (MQ=255)
                                                             cTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  <  1:3301187/57‑1 (MQ=255)
                                                               aCTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg                  >  1:3092102/1‑55 (MQ=255)
                                                                cTCACCTTGTTGGCGCTGTCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaa  <  1:614989/70‑1 (MQ=255)
                                                                cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg                             >  1:2628075/1‑43 (MQ=25)
                                                                cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg                             >  1:1214244/1‑43 (MQ=25)
                                                                cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa                >  1:106136/1‑56 (MQ=255)
                                                                cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaa  >  1:3010704/1‑70 (MQ=255)
                                                                 tCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc             >  1:2177203/1‑58 (MQ=255)
                                                                    |                                                                 
AGACGGGCGCATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAA  >  W3110S.gb/3824446‑3824578

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