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 F8 I0 R1 43 62.4 4721813 98.4% 4646263 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,824,326 T→C 100% pseudogene (459/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3260TC100.0% 293.8 / NA 83pseudogene (459/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (30/53);  total (30/53)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTG  >  W3110S.gb/3824258‑3824392
                                                                    |                                                                  
aCGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc                                                                  >  1:277540/1‑71 (MQ=255)
 cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAaaaccaaacc                                                                  <  1:3965161/70‑1 (MQ=255)
 cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc                                                                  <  1:2223459/70‑1 (MQ=255)
     tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:2266589/71‑1 (MQ=255)
      gCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             >  1:2025662/1‑70 (MQ=255)
        cTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTTGTGGAAAACGGCTAGCTGAAAACCAACCCGATGAAAg                                                          <  1:4196998/71‑1 (MQ=255)
        cTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:1045864/68‑1 (MQ=255)
        cTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:4339669/68‑1 (MQ=255)
         tGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa                                                                <  1:3974468/64‑1 (MQ=255)
         tGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGa                                                                <  1:3262209/64‑1 (MQ=255)
          gCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                         >  1:3135646/1‑70 (MQ=255)
           cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAggg                                                        <  1:2155944/70‑1 (MQ=255)
           cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                         <  1:933385/69‑1 (MQ=255)
           cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                         <  1:1400398/69‑1 (MQ=255)
           cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                         <  1:1861309/69‑1 (MQ=255)
           cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                       <  1:3404929/71‑1 (MQ=255)
            gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt                                                      <  1:4128434/71‑1 (MQ=255)
             tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                           >  1:1326844/1‑65 (MQ=255)
             tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                           >  1:4345668/1‑65 (MQ=255)
              ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                       >  1:4234403/1‑68 (MQ=255)
               gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                                   <  1:3326892/71‑1 (MQ=255)
               gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                                   <  1:4216794/71‑1 (MQ=255)
                cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                               <  1:1736731/58‑1 (MQ=255)
                cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                               <  1:3525170/58‑1 (MQ=255)
                cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                               <  1:1159118/58‑1 (MQ=255)
                cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt                                                               <  1:1139703/58‑1 (MQ=255)
                cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg                                                    >  1:2609608/1‑69 (MQ=255)
                  cTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc                                                >  1:26596/1‑71 (MQ=255)
                         aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGtt                                         <  1:4675620/71‑1 (MQ=255)
                          tGCGCTACAGAAGCTGGTGTAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc                                                >  1:4179604/1‑63 (MQ=255)
                          tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa                                                       <  1:820488/56‑1 (MQ=255)
                           gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:3913101/49‑1 (MQ=255)
                           gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc                                       >  1:535002/1‑71 (MQ=255)
                           gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc                                       >  1:305537/1‑71 (MQ=255)
                           gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc                                       >  1:2049012/1‑71 (MQ=255)
                             gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                           >  1:3439508/1‑49 (MQ=255)
                             gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg                                     <  1:41111/71‑1 (MQ=255)
                              cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt                                    <  1:3239430/71‑1 (MQ=255)
                               tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             <  1:1533061/45‑1 (MQ=255)
                               tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt                                    <  1:862920/70‑1 (MQ=255)
                                aCAGAAGCTTGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg                                                         <  1:939576/48‑1 (MQ=39)
                                aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                             >  1:624762/1‑44 (MQ=255)
                                aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg                                  >  1:2605550/1‑71 (MQ=255)
                                aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg                                  >  1:4689576/1‑71 (MQ=255)
                                 cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                 <  1:879374/71‑1 (MQ=255)
                                 cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                 <  1:3079192/71‑1 (MQ=255)
                                  aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                           >  1:4549397/1‑44 (MQ=255)
                                  aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                           >  1:2314314/1‑44 (MQ=255)
                                  aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                 >  1:627296/1‑70 (MQ=255)
                                   gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta                               >  1:601048/1‑69 (MQ=255)
                                      gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa                                                            >  1:3252470/1‑39 (MQ=255)
                                      gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta                               <  1:3523014/68‑3 (MQ=255)
                                      gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg                            <  1:1088996/71‑1 (MQ=255)
                                       cTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgt                           <  1:805309/71‑1 (MQ=255)
                                        tggtggAAAACGGCAAGCTGAAAACCAACCCGATGaaa                                                           >  1:2774313/1‑38 (MQ=255)
                                          gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                          <  1:3960378/69‑2 (MQ=255)
                                          gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                          <  1:430018/69‑2 (MQ=255)
                                          gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                          <  1:1413347/69‑2 (MQ=255)
                                           tggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                          <  1:3588770/68‑2 (MQ=255)
                                            ggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg                      >  1:4462847/1‑71 (MQ=255)
                                             gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                                        <  1:2727012/52‑1 (MQ=255)
                                              aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                 <  1:2029386/58‑1 (MQ=255)
                                              aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt                    <  1:3798818/71‑2 (MQ=255)
                                               aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                   <  1:3342841/71‑3 (MQ=255)
                                               aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                   <  1:4347890/71‑3 (MQ=255)
                                                 aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg                   >  1:1020035/1‑67 (MQ=255)
                                                  cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta                               >  1:848719/1‑54 (MQ=255)
                                                   ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAAc                       <  1:2945560/63‑1 (MQ=255)
                                                    gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca              <  1:2034617/71‑2 (MQ=255)
                                                    gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca              <  1:1235893/71‑2 (MQ=255)
                                                    gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca              <  1:1370020/71‑2 (MQ=255)
                                                      aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat            <  1:4112534/71‑4 (MQ=255)
                                                         cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta                          <  1:1418172/54‑2 (MQ=255)
                                                          tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg                            <  1:2521594/51‑1 (MQ=255)
                                                           gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc        >  1:3574604/1‑70 (MQ=255)
                                                           gAAAACCAACCCGATGAAAGGGATGGTAGACGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc        >  1:3988098/1‑70 (MQ=255)
                                                            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGttt                                        <  1:106270/37‑1 (MQ=255)
                                                            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg                                 <  1:2328407/44‑1 (MQ=255)
                                                            aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc        <  1:3142755/69‑1 (MQ=255)
                                                             aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTCTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt     >  1:4097017/1‑71 (MQ=255)
                                                                ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAAc                       <  1:3958616/50‑1 (MQ=255)
                                                                ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg  >  1:3457091/1‑71 (MQ=255)
                                                                ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg  >  1:732897/1‑71 (MQ=255)
                                                                 cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg         <  1:4711422/63‑1 (MQ=255)
                                                                 cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg         <  1:2319686/63‑1 (MQ=255)
                                                                 cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg  >  1:3041745/1‑70 (MQ=255)
                                                                    |                                                                  
ACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTG  >  W3110S.gb/3824258‑3824392

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