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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,361,585 C→T 36.1% P571P (CCG→CCA)  cadA ← lysine decarboxylase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,361,5850CT36.1% 61.9 / 60.0 61P571P (CCG→CCA) cadAlysine decarboxylase 1
Reads supporting (aligned to +/- strand):  ref base C (20/19);  new base T (15/7);  total (35/26)
Fisher's exact test for biased strand distribution p-value = 2.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTGGATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACGCAGC  >  W3110S.gb/4361515‑4361651
                                                                      |                                                                  
tgtgGATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGAc                                                                    >  1:1571425/1‑71 (MQ=255)
tgtgGATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGAc                                                                    >  1:3779241/1‑71 (MQ=255)
    gATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGgc                                                                 <  1:309940/70‑1 (MQ=255)
    gATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGgc                                                                 <  1:1313553/70‑1 (MQ=255)
        ttCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCAt                                                            >  1:948913/1‑71 (MQ=255)
        ttCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCAt                                                            >  1:2300255/1‑71 (MQ=255)
        ttCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCAt                                                            >  1:3523201/1‑71 (MQ=255)
          cTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGt                                                          >  1:1627243/1‑71 (MQ=255)
          cTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGt                                                          >  1:2531575/1‑71 (MQ=255)
          cTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGt                                                          >  1:2440828/1‑71 (MQ=255)
              gCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGttttt                                                      <  1:2330718/71‑1 (MQ=255)
                  gTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttttt                                                      <  1:3482558/67‑1 (MQ=255)
                    tCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTcaca                                                  >  1:1308604/1‑69 (MQ=255)
                    tCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTcaca                                                  >  1:456850/1‑69 (MQ=255)
                    tCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTcaca                                                  >  1:1922184/1‑69 (MQ=255)
                      cTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCa                                              <  1:1099440/71‑1 (MQ=255)
                        gAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAgg                                            >  1:1436381/1‑71 (MQ=255)
                        gAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAgg                                            >  1:3459888/1‑71 (MQ=255)
                          aTACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCACCATGTTTTTCACACGCAGGtt                                          <  1:623450/71‑1 (MQ=255)
                          aTACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGtt                                          <  1:1318771/71‑1 (MQ=255)
                             cGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttt                                                        >  1:2922158/1‑54 (MQ=255)
                             cGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttt                                                        >  1:1257545/1‑54 (MQ=255)
                             cGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAg                                       >  1:328014/1‑71 (MQ=255)
                                 tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTc                                         <  1:812670/65‑1 (MQ=255)
                                 tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTc                                         <  1:2379909/65‑1 (MQ=255)
                                 tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg                                   <  1:529608/71‑1 (MQ=255)
                                 tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCTGCATGTTTTTCACACGCAGGTTCAGGTc                                    >  1:789636/1‑70 (MQ=255)
                                 tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg                                   <  1:1133659/71‑1 (MQ=255)
                                  gTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCa                                              <  1:3206713/59‑1 (MQ=255)
                                   ttttCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGtt                                          >  1:1564450/1‑62 (MQ=255)
                                   ttttCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa                                 >  1:3925679/1‑71 (MQ=255)
                                   ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCa                                              >  1:3945492/1‑58 (MQ=255)
                                     ttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg                               >  1:233359/1‑71 (MQ=255)
                                     ttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg                               >  1:3966879/1‑71 (MQ=255)
                                     ttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg                               >  1:879678/1‑71 (MQ=255)
                                       cATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg                               <  1:3628056/69‑1 (MQ=255)
                                       cATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg                               <  1:1765098/69‑1 (MQ=255)
                                       cATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGc                              <  1:1172023/70‑1 (MQ=255)
                                        aTAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCTAACGCa                             <  1:3050210/70‑1 (MQ=255)
                                        aTAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCa                             <  1:1923356/70‑1 (MQ=255)
                                        aTAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCa                             <  1:1928050/70‑1 (MQ=255)
                                          aGAATTCAGGATCTTCACGATACAGAGATGgcagc                                                              >  1:2096479/1‑35 (MQ=255)
                                           gAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGtt                         >  1:1540119/1‑71 (MQ=255)
                                             aTTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGttt                        >  1:2605350/1‑70 (MQ=255)
                                                cAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAag                    >  1:3530921/1‑71 (MQ=255)
                                                cAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAag                    >  1:3962618/1‑71 (MQ=255)
                                                   gATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCa                             <  1:2810845/59‑1 (MQ=255)
                                                    aTCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCa                             <  1:1613800/58‑1 (MQ=255)
                                                     tCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt               >  1:375122/1‑71 (MQ=255)
                                                      cTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt               >  1:1333954/1‑70 (MQ=255)
                                                      cTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt               >  1:2204628/1‑70 (MQ=255)
                                                      cTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt               >  1:81278/1‑70 (MQ=255)
                                                      cTTCACGATACACAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACg                           >  1:3583445/1‑58 (MQ=255)
                                                        tCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTc                                         <  1:1357988/42‑1 (MQ=255)
                                                          aCGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCagag          <  1:389299/71‑1 (MQ=255)
                                                          aCGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCagag          <  1:442226/71‑1 (MQ=255)
                                                            gATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTaaa                     >  1:925612/1‑58 (MQ=255)
                                                              tACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg                                   <  1:3534510/42‑1 (MQ=255)
                                                                cAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAATGTCAGTCAGAGCACg      >  1:4009265/1‑69 (MQ=255)
                                                                cAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACg      >  1:1473840/1‑69 (MQ=255)
                                                                cAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAAAGCACGTTTAAAGTCAGTCAGAGCACg      >  1:3330248/1‑69 (MQ=255)
                                                                  gagaCGGCTGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACgcagc  <  1:2231975/71‑1 (MQ=255)
                                                                  gagaCGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACgcagc  <  1:3193104/71‑1 (MQ=255)
                                                                      |                                                                  
TGTGGATATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACGCAGC  >  W3110S.gb/4361515‑4361651

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