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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,863,059 G→A 41.4% L56L (CTG→CTA)  ygbM → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,863,0590GA41.4% 42.1 / 84.0 70L56L (CTG→CTA) ygbMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (18/23);  new base A (15/14);  total (33/37)
Fisher's exact test for biased strand distribution p-value = 6.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.74e-01

TTTCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGT  >  W3110S.gb/2862991‑2863128
                                                                    |                                                                     
tttCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAgc                                                                     >  1:4180040/1‑71 (MQ=255)
tttCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAgc                                                                     >  1:4245543/1‑71 (MQ=255)
  tCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGgcg                                                                    <  1:136952/70‑1 (MQ=255)
  tCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAgcgc                                                                   >  1:3394858/1‑71 (MQ=255)
        tCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTc                                                              <  1:380801/70‑1 (MQ=255)
         cccTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTc                                                              <  1:2743352/69‑1 (MQ=255)
          ccTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                            <  1:5133839/70‑1 (MQ=255)
          ccTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                            <  1:3183549/70‑1 (MQ=255)
            tataACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTc                                                              <  1:1259987/66‑1 (MQ=255)
            tataACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTc                                                              <  1:204583/66‑1 (MQ=255)
            tataACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTc                                                              <  1:185903/66‑1 (MQ=255)
            tataACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCaa                                                            <  1:3399418/68‑1 (MQ=255)
             ataACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTc                                                              <  1:4618062/65‑1 (MQ=255)
               aaCTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTc                                                              <  1:179444/63‑1 (MQ=255)
               aaCTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTCACACTGGCGCTGTTc                                                              >  1:2304634/1‑63 (MQ=255)
                   actCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTc                                                    <  1:3205310/69‑1 (MQ=255)
                    ctCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTcc                                                   <  1:3121564/69‑1 (MQ=255)
                      ccACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATa                                                          >  1:4625065/1‑60 (MQ=255)
                       cACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCaa                                                            >  1:2995243/1‑57 (MQ=255)
                        aCCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGgaga                                             <  1:4619192/71‑1 (MQ=255)
                          ccTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAgcg                                                                    <  1:1185014/46‑1 (MQ=255)
                           cTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCaa                                                            >  1:2390381/1‑53 (MQ=255)
                           cTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGgaga                                             >  1:1328454/1‑68 (MQ=255)
                            tGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGga                                               <  1:3425553/65‑1 (MQ=255)
                            tGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGga                                               <  1:2780848/65‑1 (MQ=255)
                            tGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGGAGatat                                          >  1:865104/1‑70 (MQ=255)
                             gCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                            >  1:888169/1‑51 (MQ=255)
                             gCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGGAGatat                                          >  1:534145/1‑69 (MQ=255)
                              cAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATAtt                                         <  1:4756284/69‑1 (MQ=255)
                              cAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATAtt                                         <  1:4342282/69‑1 (MQ=255)
                              cAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGGAGATAtt                                         <  1:2849795/69‑1 (MQ=255)
                                aaTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGgcgc                                                                   >  1:1862442/1‑41 (MQ=255)
                                aaTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATg                                     >  1:1762639/1‑71 (MQ=255)
                                 aTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                            >  1:1290451/1‑47 (MQ=255)
                                 aTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCaa                                                            >  1:1408632/1‑47 (MQ=255)
                                 aTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATAtt                                         <  1:2894646/66‑1 (MQ=255)
                                 aTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGc                                    <  1:3514658/71‑1 (MQ=255)
                                 aTCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGc                                    <  1:2497777/71‑1 (MQ=255)
                                   ccAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTa                                        >  1:3566810/1‑65 (MQ=255)
                                   ccAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTc                                                              >  1:4581090/1‑43 (MQ=255)
                                   ccAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTc                                                              >  1:1793716/1‑43 (MQ=255)
                                   ccAAAAGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTc                                                              >  1:4268914/1‑43 (MQ=255)
                                      aaaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCgggg                                >  1:3440018/1‑70 (MQ=255)
                                      aaaGCAACTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCgggg                                >  1:2504661/1‑70 (MQ=255)
                                       aaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTcc                                                   >  1:3074303/1‑50 (MQ=255)
                                       aaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAAt                                      >  1:2311985/1‑63 (MQ=255)
                                       aaGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGa                              <  1:995742/71‑1 (MQ=255)
                                           aaCTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATAc                                                         >  1:2519705/1‑40 (MQ=255)
                                           aaCTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATg                                     >  1:3206316/1‑60 (MQ=255)
                                           aaCTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATg                                     >  1:3209930/1‑60 (MQ=255)
                                            aCTGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGga                                               <  1:4348572/49‑1 (MQ=255)
                                              tGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATAtt                                         <  1:2334138/53‑1 (MQ=255)
                                              tGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATAtt                                         <  1:3946298/53‑1 (MQ=255)
                                              tGGAGCAAAACCATCTGACACTAGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGa                       >  1:2233540/1‑71 (MQ=255)
                                                gAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGAt                      >  1:1062962/1‑70 (MQ=255)
                                                       aCCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGaa                             >  1:1391312/1‑56 (MQ=255)
                                                           tCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGatat                                          <  1:357970/39‑1 (MQ=255)
                                                           tCTGACACTAGCGCTGTTCAATACCGCTCCCGGAGATAtt                                         <  1:369641/40‑1 (MQ=255)
                                                           tCTGACACTAGCGCTGTTCAATACCGCTCCCGGAGATAtt                                         <  1:1369071/40‑1 (MQ=255)
                                                              gACACTAGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATgg                          >  1:61131/1‑52 (MQ=255)
                                                              gACACTAGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATgg                          >  1:1958296/1‑52 (MQ=255)
                                                               acacTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGaa                             >  1:4140171/1‑48 (MQ=255)
                                                               acacTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTcc         <  1:1890035/68‑1 (MQ=255)
                                                               acacTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTcc         <  1:51604/68‑1 (MQ=255)
                                                               acacTAGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCg       <  1:4591739/70‑1 (MQ=255)
                                                               acacTAGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCg       <  1:4277759/70‑1 (MQ=255)
                                                                 acTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGAc    <  1:2552492/71‑1 (MQ=255)
                                                                  cTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCggggg                               <  1:4212427/43‑1 (MQ=255)
                                                                  cTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCggggg                               <  1:3929410/43‑1 (MQ=255)
                                                                   tGGCGCTGTTCAATACCGCTCACGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGt  >  1:4046745/1‑71 (MQ=255)
                                                                    |                                                                     
TTTCTGTTTCCCTATAACTACTCCACCCTGCAAATCCAAAAGCAACTGGAGCAAAACCATCTGACACTGGCGCTGTTCAATACCGCTCCCGGAGATATTAATGCGGGGGAATGGGGATTATCCGCCCTTCCCGGACGT  >  W3110S.gb/2862991‑2863128

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