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 F21 I0 R1 476 35.3 2812105 96.7% 2719305 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,103,846 T→C 86.5% Y5H (TAC→CAC)  ompR → DNA‑binding response regulator in two‑component regulatory system with EnvZ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,103,8460TC86.5% 99.6 / 7.1 37Y5H (TAC→CAC) ompRDNA‑binding response regulator in two‑component regulatory system with EnvZ
Reads supporting (aligned to +/- strand):  ref base T (2/3);  new base C (20/12);  total (22/15)
Fisher's exact test for biased strand distribution p-value = 3.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

TACACGCTTACAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACTACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACGTTATCTCACCGA  >  W3110S.gb/4103792‑4103910
                                                      |                                                                
tACACGCTTACAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACCACAAGa                                                            <  1:1821057/61‑1 (MQ=255)
  cacGCTTACAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTc                                                 >  1:1846197/1‑70 (MQ=255)
    cGCTTACAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACTACAAGATTCTGGTGGTCGAt                                              <  1:2608200/71‑1 (MQ=255)
     gCTTACAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGAt                                              <  1:1869326/70‑1 (MQ=255)
        tACAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGAt                                              <  1:616255/67‑1 (MQ=255)
         aCAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGATgac                                           <  1:2380200/69‑1 (MQ=255)
          cAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACTACAAGATTCTGGTGGTCGATgacga                                         <  1:404033/70‑1 (MQ=255)
          cAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGAt                                              >  1:531166/1‑65 (MQ=255)
           taaTTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGATgacga                                         <  1:2509526/68‑1 (MQ=255)
           aaaTTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAAACACAAGATTCTGGTGGTCGATgacga                                         <  1:1303694/69‑1 (MQ=255)
                gttgCGAACCTTTGGGAGTACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATgcgc                                  >  1:689269/1‑71 (MQ=255)
                        ccTTTGGGAGTACAAACAATGCAAGAGAACTACAAGATTCTGGTGGTCGATGACGACa                                       >  1:361299/1‑58 (MQ=255)
                                 gTACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGATgacga                                         <  1:994123/47‑1 (MQ=255)
                                  tACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGATgacg                                          <  1:1472985/45‑1 (MQ=255)
                                  tACAAACAATGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTgcgc                        <  1:2524765/63‑1 (MQ=255)
                                   acaaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATgacg                                          <  1:2075261/44‑1 (MQ=255)
                                   acaaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATTACGACATGCGCCTGCGTGCGCTGCTGGaa                >  1:1472064/1‑70 (MQ=255)
                                   acaaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACAt                                      >  1:15664/1‑48 (MQ=255)
                                   acaaacaaTGCAAGAGAACCACAAGATTCAGGTGGTCGATGACGACa                                       >  1:2272093/1‑47 (MQ=39)
                                    caaacaaTGCAAGAGAACTACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACg              >  1:394406/1‑71 (MQ=255)
                                    caaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACg              >  1:464006/1‑71 (MQ=255)
                                    caaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACg              >  1:1996107/1‑71 (MQ=255)
                                    caaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACg              >  1:107207/1‑71 (MQ=255)
                                    caaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACg              >  1:1971167/1‑71 (MQ=255)
                                    caaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACg              >  1:1406028/1‑71 (MQ=255)
                                    caaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACg              >  1:1285606/1‑71 (MQ=255)
                                    caaacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACg              >  1:1168915/1‑71 (MQ=255)
                                      aacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACAt                                      >  1:1931602/1‑45 (MQ=255)
                                      aacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCgctgc                     >  1:1090723/1‑62 (MQ=255)
                                      aacaaTGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACGt             >  1:1758449/1‑70 (MQ=255)
                                           tGCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACGTTAtct        >  1:482500/1‑70 (MQ=255)
                                            gCAAGAGAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACGTTATCTCa      >  1:2142046/1‑71 (MQ=255)
                                               agagAACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACGtt            <  1:1583947/62‑1 (MQ=255)
                                                gagaACCACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCATGCGCTGCTGGAACGTTATCTCACCGa  <  1:2422318/71‑1 (MQ=255)
                                                  gaACCACAAGATTCTGGTGGTCGATGACGACATGCGCCtgcg                             >  1:1368903/1‑42 (MQ=255)
                                                  gaACCACAAGATTCTGGTGGTCGATGACGACATGCGCCtgcg                             >  1:628810/1‑42 (MQ=255)
                                                     cTACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACGtt            <  1:1801526/56‑1 (MQ=255)
                                                      |                                                                
TACACGCTTACAAATTGTTGCGAACCTTTGGGAGTACAAACAATGCAAGAGAACTACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGTGCGCTGCTGGAACGTTATCTCACCGA  >  W3110S.gb/4103792‑4103910

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