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 2,818,985 A→G 30.0% R561R (CGT→CGC)  alaS ← alanyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,818,9850AG30.0% 50.4 / 30.4 40R561R (CGT→CGC) alaSalanyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base A (13/15);  new base G (7/5);  total (20/20)
Fisher's exact test for biased strand distribution p-value = 7.31e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01

CGATACATGAGTACCCAGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCAGAGAACCCGCA  >  W3110S.gb/2818919‑2819054
                                                                  |                                                                     
cGATACATGAGTACCCAGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGaa                                                                   <  1:805349/71‑1 (MQ=255)
  aTACATGAGTACCCAGAACCTGTCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGGCGAATa                                                                 <  1:331719/71‑1 (MQ=255)
         aGTACCCAGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGGGGAGTGATTCAGGCGAATACGGgcgc                                                          >  1:4476612/1‑71 (MQ=255)
          gTACCCAGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGgcgc                                                          >  1:585487/1‑70 (MQ=255)
             cccAGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACg                                                               >  1:285144/1‑62 (MQ=255)
             cccAGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGcgac                                                       >  1:2494472/1‑70 (MQ=255)
              ccAGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGcgacga                                                     <  1:2144154/71‑1 (MQ=255)
                aGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGGCGAATACGGGCGCGACGAGc                                                   >  1:246359/1‑71 (MQ=255)
                  aaCCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGcgacga                                                     <  1:3983205/67‑1 (MQ=255)
                  aaCCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGcgacga                                                     <  1:2069321/67‑1 (MQ=255)
                   aCCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGcgacga                                                     <  1:2069323/66‑1 (MQ=255)
                   aCCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCt                                                 >  1:3574699/1‑70 (MQ=255)
                   aCCTGGCGCAGCGAAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCt                                                 >  1:3718385/1‑70 (MQ=255)
                       ggCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCtcatc                                             >  1:2419570/1‑70 (MQ=255)
                          gcagcgcagcGTGCATCAGGTGCGTTGCGGAGTGATTCAGGCGaa                                                                   <  1:4587971/45‑1 (MQ=255)
                          gcagcgcagcGTGCATCAGGTGCGTTGCGGAGTGATTCAGGCGAATACGGGCGCGACGAGCCTCATCAACa                                         <  1:4263694/71‑1 (MQ=255)
                               gcagcgTGCATCAGGTGCGTTGCGGAGTGATTCAGACGaa                                                                   >  1:3799821/1‑40 (MQ=255)
                                cagcgTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCt                                                 >  1:78570/1‑57 (MQ=255)
                                  gcgTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGcgcg                                                         <  1:2925573/47‑1 (MQ=255)
                                         tCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGcgacga                                                     <  1:3317600/44‑1 (MQ=255)
                                               gCGTTGCGGAGTGATTCAGGCGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGcc                     >  1:2687533/1‑70 (MQ=255)
                                                cGTTGCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCt                                                 <  1:2740858/41‑1 (MQ=255)
                                                cGTTGCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCa                   <  1:1294016/71‑1 (MQ=255)
                                                  ttGCGGAGTGATTCAGGCGAATACGGGCGCGACGAGCCTCATCaa                                           <  1:1829795/45‑1 (MQ=255)
                                                  ttGCGGAGTGATTCAGGCGAATACGGGCGCGACGAGCCTCATCaa                                           <  1:4349939/45‑1 (MQ=255)
                                                   tGCGGAGTGATTCAGGCGAATACGGGCGCGACGAGCCTCATCAACATCAGcc                                   >  1:2863259/1‑52 (MQ=255)
                                                    gCGGAGTGATTCAGGCGAATACGGGCGCGACGAGCCTCATCAACATCAGCCt                                  >  1:4428995/1‑52 (MQ=255)
                                                    gCGGAGTGATTCAGGCGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACttt               >  1:1161909/1‑71 (MQ=255)
                                                    gCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACttt               >  1:4081193/1‑71 (MQ=255)
                                                    gCGGAGTGATTCAGACGAATACGGGAGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACttt               >  1:1656318/1‑71 (MQ=255)
                                                     cGGAGTGATTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTc              <  1:1735841/71‑1 (MQ=255)
                                                        aGTGATTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGcc                                   >  1:1843428/1‑47 (MQ=255)
                                                         gTGATTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCagag          <  1:4137387/71‑1 (MQ=255)
                                                          tGATTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCAgaga         <  1:4128247/71‑1 (MQ=255)
                                                            aTTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCAGAGAAc       >  1:3910492/1‑71 (MQ=255)
                                                             ttCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACcgc                           <  1:16924/50‑1 (MQ=255)
                                                               cAGGCGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCAGAGAACCCg    >  1:3635389/1‑71 (MQ=255)
                                                               cAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGcc                                   >  1:2348865/1‑40 (MQ=255)
                                                                aGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCAGAGAACCCg    <  1:4576075/70‑1 (MQ=255)
                                                                 gACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCagag          <  1:2807897/63‑1 (MQ=255)
                                                                  aCGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCAGAGAACCCgca  <  1:476829/70‑1 (MQ=255)
                                                                  |                                                                     
CGATACATGAGTACCCAGAACCTGGCGCAGCGCAGCGTGCATCAGGTGCGTTGCGGAGTGATTCAGACGAATACGGGCGCGACGAGCCTCATCAACATCAGCCTGCACCGCGTCGCCCACTTTCAGAGAACCCGCA  >  W3110S.gb/2818919‑2819054

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