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 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,657,562 T→C 54.4% I14T (ATT→ACT)  ynfB → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,657,5620TC54.4% 17.7 / 74.3 57I14T (ATT→ACT) ynfBhypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (13/13);  new base C (10/21);  total (23/34)
Fisher's exact test for biased strand distribution p-value = 1.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAG  >  W3110S.gb/1657497‑1657629
                                                                 |                                                                   
tAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTActct                                                                  >  1:3648705/1‑69 (MQ=255)
tAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTActct                                                                  >  1:665906/1‑69 (MQ=255)
        catACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCtt                                                          >  1:1052548/1‑69 (MQ=255)
        catACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCtt                                                          >  1:2923860/1‑69 (MQ=255)
        catACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCtt                                                          >  1:2371697/1‑69 (MQ=255)
        catACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCtt                                                          >  1:937273/1‑69 (MQ=255)
        catACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCtt                                                          >  1:2228370/1‑69 (MQ=255)
        catACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCt                                                           >  1:3110116/1‑68 (MQ=255)
           aCAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTgcg                                                       >  1:858834/1‑69 (MQ=255)
           aCAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTgcg                                                       >  1:1415771/1‑69 (MQ=255)
           aCAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTgc                                                        >  1:2844682/1‑68 (MQ=255)
           aCAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTgc                                                        >  1:1394881/1‑68 (MQ=255)
           aCAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTgcg                                                       <  1:2712974/69‑1 (MQ=255)
                gaatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTgcg                                                       >  1:2290762/1‑64 (MQ=255)
                 aatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTgg                                                 <  1:713443/69‑1 (MQ=255)
                 aatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTgg                                                 <  1:647349/69‑1 (MQ=255)
                 aatgaatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTgg                                                 <  1:2272355/69‑1 (MQ=255)
                  atgaatTATGAAAATCACTCTCAGCAAACGAATCTGCCTGCTCGCTACTCTGCTGCCTTgcg                                                       >  1:1569020/1‑62 (MQ=255)
                     aatTATGTAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTct                                                                  <  1:2982312/48‑1 (MQ=255)
                     aatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCa                                               >  1:3537836/1‑67 (MQ=255)
                     aatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCa                                               >  1:1985486/1‑67 (MQ=255)
                     aatTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCa                                               >  1:2343238/1‑67 (MQ=255)
                         aTGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCAtt                                             <  1:3486382/65‑1 (MQ=255)
                         aTGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCAtt                                             <  1:2278215/65‑1 (MQ=255)
                         aTGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCAtt                                             <  1:2857490/65‑1 (MQ=255)
                         aTGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAg                                          >  1:1796296/1‑68 (MQ=255)
                          tGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTTCGCACTGGCATTGAGc                                         >  1:743111/1‑68 (MQ=255)
                            aaaaTCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGcaca                                      <  1:3103812/69‑1 (MQ=255)
                            aaaaTCACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGcaca                                      <  1:1635049/69‑1 (MQ=255)
                                 cACTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTgcg                                                       >  1:777050/1‑47 (MQ=255)
                                  aCTCTCAGCAAACGAATCGGCCTGCTCGCTATTct                                                                  <  1:977973/35‑1 (MQ=255)
                                  aCTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                                <  1:3669392/69‑1 (MQ=255)
                                  aCTCTCAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                                <  1:1799988/69‑1 (MQ=255)
                                     ctcAGCAAACGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCAt                             <  1:3098600/69‑1 (MQ=255)
                                          cAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                        <  1:2681587/69‑1 (MQ=255)
                                          cAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                        <  1:1132094/69‑1 (MQ=255)
                                          cAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                        <  1:2158687/69‑1 (MQ=255)
                                           aaaCGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTgg                                                 <  1:3509966/43‑1 (MQ=255)
                                           aaaCGAATCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGa                        <  1:3666413/68‑1 (MQ=255)
                                                 aTCGGCCTGCTCGGTATTCTGCTGCCTTGCGCACTgg                                                 <  1:1408904/37‑1 (MQ=255)
                                                 aTCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                                <  1:2117126/54‑1 (MQ=255)
                                                  tCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa                <  1:362166/69‑1 (MQ=255)
                                                  tCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa                <  1:423657/69‑1 (MQ=255)
                                                  tCGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa                <  1:849097/69‑1 (MQ=255)
                                                   cGGCCTGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACaa               <  1:3299648/69‑1 (MQ=255)
                                                        tGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTgg          <  1:2039887/69‑1 (MQ=255)
                                                        tGCTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTg           >  1:2751311/1‑68 (MQ=255)
                                                          cTCGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTg        >  1:2431435/1‑69 (MQ=255)
                                                            cGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa                <  1:1464143/59‑1 (MQ=255)
                                                            cGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACa                <  1:819686/59‑1 (MQ=255)
                                                            cGCTACTCTGCTGCCTTGCTCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTg        <  1:177856/67‑1 (MQ=255)
                                                            cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGcac                                       >  1:3117147/1‑36 (MQ=255)
                                                            cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGcac                                       >  1:180122/1‑36 (MQ=255)
                                                            cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGcac                                       >  1:369071/1‑36 (MQ=255)
                                                            cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                                <  1:1847942/43‑1 (MQ=255)
                                                            cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                                <  1:595421/43‑1 (MQ=255)
                                                            cGCTACTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGtt                                <  1:418323/43‑1 (MQ=255)
                                                                aTTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAg  <  1:2531440/69‑1 (MQ=255)
                                                                aTTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAg  <  1:1914006/69‑1 (MQ=255)
                                                                 |                                                                   
TAATCATTCATACAGGGAATGAATTATGAAAATCACTCTCAGCAAACGAATCGGCCTGCTCGCTATTCTGCTGCCTTGCGCACTGGCATTGAGCACAACTGTTCATGCCGAAACTAACAAACTGGTGATTGAG  >  W3110S.gb/1657497‑1657629

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