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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 651,069 T→C 37.3% N4S (AAT→AGT)  citC ← citrate lyase synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb651,0690TC37.3% 56.9 / 71.1 67N4S (AAT→AGT) citCcitrate lyase synthetase
Reads supporting (aligned to +/- strand):  ref base T (20/22);  new base C (10/15);  total (30/37)
Fisher's exact test for biased strand distribution p-value = 6.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

TTCATGCAGGAATTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAATGTTGTTCAATG  >  W3110S.gb/650999‑651138
                                                                      |                                                                     
ttCATGCAGGAATTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCAt                                                                       >  1:4894025/1‑71 (MQ=255)
ttCATGCAGGAATTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCAt                                                                       >  1:4888501/1‑71 (MQ=255)
 tCATGCAGGAATTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCAtt                                                                      >  1:77194/1‑71 (MQ=255)
 tCATGCAGGAATTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCAtt                                                                      >  1:1972662/1‑71 (MQ=255)
      cAGGAATTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGa                                                                 <  1:3593382/71‑1 (MQ=255)
       aGGAATTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGGGAAAATATCATTGCCGa                                                                 <  1:2992091/70‑1 (MQ=255)
           aTTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACata                                                            <  1:179050/71‑1 (MQ=255)
               ggCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACAtaataa                                                        <  1:2628892/71‑1 (MQ=255)
               ggCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACAtaataa                                                        <  1:4746629/71‑1 (MQ=255)
                gCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACataata                                                         <  1:3305689/69‑1 (MQ=255)
                gCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATaataaa                                                       <  1:3041086/71‑1 (MQ=255)
                gCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATaataaa                                                       <  1:968501/71‑1 (MQ=255)
                 cGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATaataaat                                                      <  1:4742107/71‑1 (MQ=255)
                  gATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATaataaa                                                       >  1:50383/1‑69 (MQ=255)
                    tttCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCAt                                                                       >  1:57018/1‑51 (MQ=255)
                    tttCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCAt                                                                       >  1:700082/1‑51 (MQ=255)
                     ttCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTa                                                  >  1:836433/1‑71 (MQ=255)
                     ttCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTa                                                  >  1:830550/1‑71 (MQ=255)
                     ttCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTa                                                  >  1:4686652/1‑71 (MQ=255)
                      tCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTa                                                  <  1:1032722/70‑1 (MQ=255)
                      tCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTAt                                                 >  1:4088012/1‑71 (MQ=255)
                        cGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATc                                                <  1:4902735/70‑1 (MQ=255)
                           cATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTg                                             >  1:2542206/1‑70 (MQ=255)
                           cATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTg                                             >  1:2649681/1‑70 (MQ=255)
                            aTTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGaa                                           <  1:1386075/71‑1 (MQ=255)
                             tttttttATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGa                                            <  1:26795/69‑1 (MQ=255)
                              ttttttATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGa                                            <  1:4797209/68‑1 (MQ=255)
                              ttttttATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGa                                            <  1:1203954/68‑1 (MQ=255)
                               tttttATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGAAgg                                         <  1:951222/70‑1 (MQ=255)
                                  ttATTTTCTGAACGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTa                                                  <  1:2828645/58‑1 (MQ=255)
                                     ttttCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCAtgt                                  <  1:3801170/71‑1 (MQ=255)
                                            aaCGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTa                             <  1:2778768/69‑1 (MQ=255)
                                             aCGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCg                          <  1:4240229/71‑1 (MQ=255)
                                             aCGTTTTACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCg                          <  1:108779/71‑1 (MQ=255)
                                              cGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCAtgttg                                >  1:706920/1‑64 (MQ=255)
                                              cGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCAtgttg                                >  1:1875016/1‑64 (MQ=255)
                                              cGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCAtgttg                                >  1:334250/1‑64 (MQ=255)
                                              cGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCAtgttg                                >  1:1438806/1‑64 (MQ=255)
                                                ttttACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGAtt                       >  1:3477599/1‑71 (MQ=255)
                                                 tttACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCAtg                                   <  1:4241786/58‑1 (MQ=255)
                                                 tttACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTAt                                                 <  1:4810436/44‑1 (MQ=255)
                                                 tttACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGAttt                      >  1:483379/1‑71 (MQ=255)
                                                  ttACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGt                                                   >  1:4014290/1‑41 (MQ=255)
                                                  ttACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGt                                                   >  1:4344482/1‑41 (MQ=255)
                                                  ttACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGAAgg                                         >  1:3204524/1‑51 (MQ=255)
                                                  ttACGCGGGTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTg                     >  1:2868766/1‑71 (MQ=255)
                                                    aCGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGc                    <  1:1895991/70‑1 (MQ=255)
                                                        gggTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGa               <  1:994173/71‑1 (MQ=255)
                                                         ggTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGctt                                    <  1:3145390/49‑3 (MQ=255)
                                                         ggTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCAt                                    <  1:180979/49‑1 (MQ=255)
                                                          gTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAAt             >  1:4575914/1‑71 (MQ=255)
                                                          gTGAAAATATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAAt             >  1:5007658/1‑71 (MQ=255)
                                                           tGAAAATATCACTGCCGAACATAATAAATAGTATCCTg                                             <  1:4236171/38‑1 (MQ=255)
                                                           tGAAAATATCACTGCCGAACATAATAAATAGTATCCTg                                             <  1:2884332/38‑1 (MQ=255)
                                                            gAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAAtgt           >  1:4984920/1‑71 (MQ=255)
                                                            gAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAAtgt           >  1:3580356/1‑71 (MQ=255)
                                                            gAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAAtgt           >  1:2136085/1‑71 (MQ=255)
                                                             aaaaTATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGAt                        <  1:4246352/57‑1 (MQ=255)
                                                              aaaTATCATTGCCGAACATAATAAATAGTATCCTGaa                                           >  1:1900991/1‑37 (MQ=255)
                                                              aaaTATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCaa                  >  1:1479677/1‑62 (MQ=255)
                                                              aaaTATCACTGCCGAACATAATAAATAGTATCCTGAAGGTg                                       >  1:4215150/1‑41 (MQ=255)
                                                              aaaTATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAAtgttg         >  1:3122409/1‑71 (MQ=255)
                                                               aaTATCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGAt                        <  1:3390565/55‑1 (MQ=255)
                                                                 tatCATTGCCGAACATAATAAATAGTATCCTGAAGGTGc                                      <  1:2157739/39‑1 (MQ=255)
                                                                  atCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGc                    <  1:1069923/56‑1 (MQ=255)
                                                                  atCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGc                    <  1:912781/56‑1 (MQ=255)
                                                                   tCACTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAATGTTGTTCaa    <  1:2885524/71‑1 (MQ=255)
                                                                     aTTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGaa              >  1:2137224/1‑59 (MQ=255)
                                                                     aTTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGaa              >  1:2304637/1‑59 (MQ=255)
                                                                     aTTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGaa              >  1:3740041/1‑59 (MQ=255)
                                                                     aTTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAATGTTGTTCAATg  <  1:2352832/71‑1 (MQ=255)
                                                                     aTTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAATGTTGTTCAATg  >  1:3620908/1‑71 (MQ=255)
                                                                     aTTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAATGTTGTTCAATg  <  1:98108/71‑1 (MQ=255)
                                                                      |                                                                     
TTCATGCAGGAATTGGGCGATTTCCGCCATTTTTTTATTTTCTGAACGTTTTACGCGGGTGAAAATATCATTGCCGAACATAATAAATAGTATCCTGAAGGTGCATGTTGTTATCGATTTGCAACGAATGTTGTTCAATG  >  W3110S.gb/650999‑651138

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