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 1,237,778 C→T 9.7% R347R (CGG→CGA)  ycgB ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,237,7780CT 9.7% 120.6 / 3.2 41R347R (CGG→CGA) ycgBconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (25/12);  new base T (2/2);  total (27/14)
Fisher's exact test for biased strand distribution p-value = 5.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

TCCAGCCAGTCGGAACCGGCGATATCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCGCTGTACCACGGGCTGTTA  >  W3110S.gb/1237710‑1237847
                                                                    |                                                                     
tCCAGCCAGTCGGAACCGGCGATATCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCg                                                                     >  1:966418/1‑71 (MQ=255)
tCCAGCCAGTCGGAACCGGCGATATCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCg                                                                     >  1:1541490/1‑71 (MQ=255)
       agTCGGAACCGGCGATATCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAata                                                              <  1:1355180/71‑1 (MQ=255)
          cGGAACCGGCGATATCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATcc                                                           >  1:1176402/1‑71 (MQ=255)
                 ggCGATATCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACa                                                    <  1:1148268/71‑1 (MQ=255)
                       atCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCg                                               >  1:265470/1‑70 (MQ=255)
                       atCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCg                                               >  1:1826227/1‑70 (MQ=255)
                       atCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCg                                               >  1:1645759/1‑70 (MQ=255)
                       atCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCG‑TTAATATCCTGGAACATGGCGaa                                             >  1:1939991/1‑71 (MQ=255)
                        tCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATTCGTTTAATATCCTGGAACATGGCGaa                                             >  1:1893987/1‑71 (MQ=255)
                                ccAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAggg                                     <  1:1396712/71‑1 (MQ=255)
                                  aGTATTTGTCTTCTTCCGTTGGCGACTGACAAATTCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCa                                   <  1:546776/71‑1 (MQ=255)
                                   gTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACa                                                    <  1:3126204/53‑1 (MQ=255)
                                    tATTTGTCTTCTTCCGTTGGCGACTGACAAATTCGTTTAATATCCTCGAACa                                                    <  1:3967746/52‑1 (MQ=39)
                                    tATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAAccc                                          <  1:2875742/62‑1 (MQ=255)
                                      tttGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTaa                                                                >  1:3536565/1‑38 (MQ=255)
                                      tttGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATc                                                            >  1:644720/1‑42 (MQ=255)
                                      tttGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATc                                                            >  1:378089/1‑42 (MQ=255)
                                      tttATCTTCTTCCGTTGGCGACTGACAAATCCGTTTAat                                                               >  1:1141700/1‑39 (MQ=255)
                                        tGTCTTGTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACa                                                    >  1:521323/1‑48 (MQ=255)
                                        tGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAatat                                                             >  1:3991962/1‑39 (MQ=255)
                                        tGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAggg                                     >  1:2175042/1‑63 (MQ=255)
                                        tGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAggg                                     >  1:4045445/1‑63 (MQ=255)
                                        tGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACggg                             >  1:935678/1‑71 (MQ=255)
                                        tGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACggg                             >  1:653852/1‑71 (MQ=255)
                                          tcttctTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGCACATGGCGAACCCGAGGGCATACGGGtt                           <  1:762810/71‑1 (MQ=255)
                                          tcttctTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGtt                           <  1:2353581/71‑1 (MQ=255)
                                            ttcttcCGTTGGCGACTGACAAATCCGTTTAATATCCTGGaa                                                      <  1:2097283/42‑1 (MQ=255)
                                            ttcttcCGTTGGCGACTGACAAATCCGTTTAATATCCTGGaa                                                      <  1:3851663/42‑1 (MQ=255)
                                            ttcttcCGTTGCCGACTGACAAATCCGTTTAATATCCTGGaa                                                      <  1:2204650/42‑1 (MQ=255)
                                              cttcCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACa                                                    >  1:997044/1‑42 (MQ=255)
                                              cttcCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGAt                        <  1:3015145/70‑1 (MQ=255)
                                              cttcCGTTGGCGACTGACAAATCCGTTTAATATACTGGAACa                                                    >  1:1595328/1‑42 (MQ=255)
                                                 ccGTTGGCGACTGACAAATTCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCg                    >  1:3418094/1‑71 (MQ=255)
                                                      ggCGACTGACAAATCCGTTTAATATCCTGGAACATgg                                                 >  1:2994499/1‑37 (MQ=255)
                                                      ggCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCGCTGTa               >  1:1845015/1‑71 (MQ=255)
                                                             gACAAATCCGTATAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCGCTGTACCACgg         >  1:1782228/1‑70 (MQ=255)
                                                              aCAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCGCTGTACCACGGGc       >  1:100185/1‑71 (MQ=255)
                                                              aCAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCGCTGTACCACGGGc       >  1:2983678/1‑71 (MQ=255)
                                                                aaaTCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCGCTGTACCACGGGCTg     >  1:3720198/1‑71 (MQ=255)
                                                                   tCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCGATGTACCACGGGCTGTta  <  1:1619092/71‑1 (MQ=255)
                                                                    |                                                                     
TCCAGCCAGTCGGAACCGGCGATATCCGGGAACCAGTATTTGTCTTCTTCCGTTGGCGACTGACAAATCCGTTTAATATCCTGGAACATGGCGAACCCGAGGGCATACGGGTTGATGCCGCTGTACCACGGGCTGTTA  >  W3110S.gb/1237710‑1237847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A