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
A19 F48 I1 R1 83 81.6 2760494 99.1% 2735649 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 319,723 G→T D93E (GAC→GAA)  rclA ← putative pyridine nucleotide‑disulfide oxidoreductase RclA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913319,7230GT98.0% 172.6 / ‑4.0 51D93E (GAC→GAA) rclAputative pyridine nucleotide‑disulfide oxidoreductase RclA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base T (26/24);  minor base C (1/0);  total (27/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

CAGGAATTGGCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACGTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTTTGGTTGGGATGC  >  NC_000913/319590‑319859
                                                                                                                                     |                                                                                                                                        
cAGGAATTGGCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGata                                                                                                                                    <  2:864335/140‑1 (MQ=255)
cAGGAATTGGCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGata                                                                                                                                    <  2:1356743/140‑1 (MQ=255)
aaGGAATTGGCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGata                                                                                                                                    <  2:239624/139‑1 (MQ=255)
 aGGAATTGGCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGatat                                                                                                                                   >  1:1239054/1‑140 (MQ=255)
 aGGAATTGGCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGatat                                                                                                                                   <  2:586547/140‑1 (MQ=255)
 aGGAATTGGCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACCTCGatat                                                                                                                                   >  1:168157/1‑140 (MQ=255)
        ggCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCat                                                                                                                            <  2:1101299/140‑1 (MQ=255)
             aaCCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCg                                                                                                                       <  2:1037312/140‑1 (MQ=255)
              aCCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGc                                                                                                                      >  1:606425/1‑140 (MQ=255)
                  cGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGa                                                                                                                  <  1:197904/140‑1 (MQ=255)
                   ggTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGAt                                                                                                                 <  1:1249581/140‑1 (MQ=255)
                         tgCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGaa                                                                                                           <  1:218875/140‑1 (MQ=255)
                             ccGGTATTAATAAAAATTTGCTCGCCATGAATGTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAAtt                                                                                                       >  1:1297588/1‑140 (MQ=255)
                              cGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAAttt                                                                                                      >  2:538308/1‑139 (MQ=255)
                              cGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTc                                                                                                      >  1:1149900/1‑140 (MQ=255)
                                 tATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCtta                                                                                                   >  1:228778/1‑140 (MQ=255)
                                   ttAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCttatt                                                                                                 >  1:696503/1‑140 (MQ=255)
                                        aaaaaTTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTa                                                                                            <  2:1239054/140‑1 (MQ=255)
                                        aaaaaTTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACCTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTa                                                                                            <  2:168157/140‑1 (MQ=255)
                                        aaaaaTTTTCTCGCCATGAATTTCAAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTa                                                                                            >  2:453782/1‑140 (MQ=255)
                                           aaTTTTCTCGCCATGAATTGCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGGCGATCACTTCGATA‑TGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTaaaaa                                                                                        >  1:1297530/1‑140 (MQ=255)
                                                            tttCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCAttt                                                                        <  1:681294/140‑1 (MQ=255)
                                                                 aGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACg                                                                   <  1:269945/140‑1 (MQ=255)
                                                                 aGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACg                                                                   <  1:538308/140‑1 (MQ=255)
                                                                 aGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACg                                                                   <  2:51320/140‑1 (MQ=255)
                                                                           cAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCa                                                         <  2:1149900/140‑1 (MQ=255)
                                                                            aGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCAc                                                        >  1:35849/1‑140 (MQ=255)
                                                                            aGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCAc                                                        >  1:1193534/1‑140 (MQ=255)
                                                                              gCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACgg                                                      >  2:707001/1‑140 (MQ=255)
                                                                               ccGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGa                                                     <  2:888323/140‑1 (MQ=255)
                                                                                     aaCACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAAt                                               <  1:9672/140‑1 (MQ=255)
                                                                                      acacGCAGGCTATGATTAGTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATc                                              >  1:1245196/1‑140 (MQ=255)
                                                                                         cGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCtgt                                           >  1:767635/1‑140 (MQ=255)
                                                                                            aGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCtgtgtg                                        <  1:707001/140‑1 (MQ=255)
                                                                                                  tGATTATTGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAGATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGctgctg                                  <  1:937364/140‑1 (MQ=255)
                                                                                                      tattGATAAACTCCGCCTGGTCGTCGATAACTTCAATATTCGACATATCAGCTAGATTCCGAAGATTCTTATTAAGTAAACACTTATAACCTACATTTTTCCCCTGCATGGCCCGGACACAATCTGTGTGCTCCTGTGCg                              <  2:1297588/140‑1 (MQ=255)
                                                                                                      tattGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCg                              >  1:101187/1‑140 (MQ=255)
                                                                                                      tattGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCg                              >  2:191837/1‑140 (MQ=255)
                                                                                                        ttGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTc                            >  2:1170188/1‑140 (MQ=255)
                                                                                                        ttGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTc                            >  1:185713/1‑140 (MQ=255)
                                                                                                        ttGATAAACTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTc                            >  1:1246551/1‑140 (MQ=255)
                                                                                                              aaCTCCGCCTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAAc                      >  2:770214/1‑140 (MQ=255)
                                                                                                                     ccTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGtt               >  1:406775/1‑140 (MQ=255)
                                                                                                                     ccTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGtt               >  1:216331/1‑140 (MQ=255)
                                                                                                                     ccTGGCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGtt               <  1:635710/140‑1 (MQ=255)
                                                                                                                         gCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTttgt           >  2:525276/1‑139 (MQ=255)
                                                                                                                         gCCGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTttgg           >  2:1329342/1‑140 (MQ=255)
                                                                                                                          ccGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTttggt          >  1:587554/1‑140 (MQ=255)
                                                                                                                          ccGTCGATCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTttggt          >  1:1148963/1‑140 (MQ=255)
                                                                                                                                aTCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTTTGGTTGGGAt    <  1:396319/140‑1 (MQ=255)
                                                                                                                                 tCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTTTGGTTGGGATg   <  1:453782/140‑1 (MQ=255)
                                                                                                                                 tCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTTTGGTTGGGATg   <  1:386339/140‑1 (MQ=255)
                                                                                                                                 tCACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTTTGGTTGGGATg   <  1:1329342/140‑1 (MQ=255)
                                                                                                                                  cACTTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTTTGGTTGGGATGc  <  2:228778/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                        
CAGGAATTGGCGGAACCACGGTTTGTGCACCGGTATTAATAAAAATTTTCTCGCCATGAATTTCCAGATTTCCCTCAGGCCGATGAACACGCAGGCTATGATTATTGATAAACTCCGCCTGGCCGTCGATCACGTCGATATTGGGCATATCCGCAAGATTATGAAAATTCTTATTACGTAAAAAATTAACCACTTCATTTTTACGCTGTATGGCACGGACAAAATCTGTGTGCTGCTGTGCGTCATGAACCAATGTTTTGGTTGGGATGC  >  NC_000913/319590‑319859

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A