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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,482,473 A→G 8.5% L174P (CTC→CCC)  argI ← ornithine carbamoyltransferase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,482,4730AG 8.5% 158.5 / 6.4 59L174P (CTC→CCC) argIornithine carbamoyltransferase 1
Reads supporting (aligned to +/- strand):  ref base A (22/32);  new base G (3/2);  total (25/34)
Fisher's exact test for biased strand distribution p-value = 6.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.31e-01

AGCTTCCGGCCAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCC  >  W3110S.gb/4482406‑4482543
                                                                   |                                                                      
aGCTTCCGGCCAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCa                                                                     <  1:3456531/71‑1 (MQ=255)
     ccGGCCAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCg                                                                  <  1:2628302/69‑1 (MQ=255)
     ccGGCCAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCg                                                                  <  1:1940501/69‑1 (MQ=255)
         ccAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGc                                                            >  1:1350514/1‑71 (MQ=255)
          cAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGcc                                                           <  1:3491145/71‑1 (MQ=255)
           aGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGcc                                                           >  1:1699688/1‑70 (MQ=255)
             cACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                >  1:51090/1‑63 (MQ=255)
              aCGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtg                                                       >  1:4111527/1‑71 (MQ=255)
              aCGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCACAt                                                        <  1:3831163/70‑1 (MQ=255)
               cGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                >  1:2771012/1‑61 (MQ=255)
               cGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgt                                                      >  1:2400721/1‑71 (MQ=255)
               cGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgt                                                      >  1:2147171/1‑71 (MQ=255)
                  ttGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAAt                                                               >  1:1176176/1‑59 (MQ=255)
                    gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                   <  1:1331894/69‑1 (MQ=255)
                    gtgGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTa                                                 >  1:575686/1‑71 (MQ=255)
                         gcgACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGGGCATCGAATTGCCCATGTTGTTAcgcgc                                            <  1:3945762/71‑1 (MQ=255)
                          cgACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgtt                                                     <  1:1798146/61‑1 (MQ=255)
                            aCCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGGGCATCg                                                                  <  1:1909094/46‑1 (MQ=255)
                            aCCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTc                                         <  1:895442/71‑1 (MQ=255)
                            aCCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTc                                         <  1:1222165/71‑1 (MQ=255)
                              cAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGGGCATCGaa                                                                >  1:3204772/1‑46 (MQ=255)
                              cAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGGGCATCGAATTGCCCATGTTGTTACGCGCGTCAc                                       >  1:3247205/1‑71 (MQ=255)
                                   gCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGaa                                                                >  1:3473051/1‑41 (MQ=255)
                                      aaTCCAGACCGGTAAGCGCCGCAGCTTCGATCATCGAATTGCCCAtgtt                                                     <  1:4613067/49‑1 (MQ=255)
                                      aaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                   <  1:2505319/51‑1 (MQ=255)
                                      aaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgtt                                                     <  1:3969846/49‑1 (MQ=255)
                                      aaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgtt                                                     <  1:4042076/49‑1 (MQ=255)
                                      aaTCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgtt                                                     <  1:3607196/49‑1 (MQ=255)
                                          cAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCa                                  >  1:1684648/1‑64 (MQ=255)
                                            gACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGt                                          <  1:1791403/54‑1 (MQ=255)
                                             aCCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGAc                             >  1:4485414/1‑66 (MQ=255)
                                                ggTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCAtgttgt                                                   <  1:3067262/41‑1 (MQ=255)
                                                ggTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCa                     <  1:3884810/71‑1 (MQ=255)
                                                 gTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAt                    <  1:1189041/71‑1 (MQ=255)
                                                  tAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTc                      <  1:200660/68‑1 (MQ=255)
                                                  tAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAtt                   >  1:1070178/1‑71 (MQ=255)
                                                   aaGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTAcg                                               >  1:3949009/1‑42 (MQ=255)
                                                   aaGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCAttt                  >  1:4240886/1‑71 (MQ=255)
                                                    aGCGCCGCAGCTTCGGGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCa                           >  1:3609974/1‑61 (MQ=255)
                                                    aGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                 <  1:108090/71‑1 (MQ=255)
                                                     gcgcCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTa                                                 <  1:2961969/38‑1 (MQ=255)
                                                      ggccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAg                               <  1:2358581/54‑1 (MQ=255)
                                                       gccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTa                                                 >  1:79301/1‑36 (MQ=255)
                                                       gccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGt               >  1:2746133/1‑70 (MQ=255)
                                                        ccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGtt              <  1:4389223/70‑1 (MQ=255)
                                                        ccgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTg             <  1:197923/71‑1 (MQ=255)
                                                         cgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCa                                  >  1:3338780/1‑49 (MQ=255)
                                                         cgcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGa            <  1:1952843/71‑1 (MQ=255)
                                                          gcAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACATGCATAGACCAGc                         >  1:1031516/1‑57 (MQ=255)
                                                           cAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc          >  1:326331/1‑71 (MQ=255)
                                                           cAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAAc          >  1:2266554/1‑71 (MQ=255)
                                                             gCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCa                                  <  1:1238811/45‑1 (MQ=255)
                                                             gCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCa                                  <  1:811566/45‑1 (MQ=255)
                                                              cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCAc                                       <  1:60314/39‑1 (MQ=255)
                                                              cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCAt                                 <  1:3484468/45‑1 (MQ=255)
                                                              cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTc                 <  1:754778/61‑1 (MQ=255)
                                                              cTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGtt              <  1:1843797/64‑1 (MQ=255)
                                                               ttCGAGCATCGAATTGCCCATGTTGTTACGCGCGTc                                         <  1:2027374/36‑1 (MQ=255)
                                                                tCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGa                              >  1:1449967/1‑46 (MQ=255)
                                                                   aGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGcc  <  1:1485247/71‑1 (MQ=255)
                                                                   |                                                                      
AGCTTCCGGCCAGCACGCTTGTGGCGCGACCAGACGCAAATCCAGACCGGTAAGCGCCGCAGCTTCGAGCATCGAATTGCCCATGTTGTTACGCGCGTCACCTGCATAGACCAGCGTCATTTCGTTGAACGCTTTGCC  >  W3110S.gb/4482406‑4482543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A