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 F1 I1 R1	315	33.5	1889570	98.7%	1865005	80.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,875,384	G→A	Q65* (CAA→TAA)	nimR ←	DNA‑binding transcriptional repressor NimR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,875,384	0	G	A	96.0%	80.3 / ‑3.7	25	Q65* (CAA→TAA)	nimR	DNA‑binding transcriptional repressor NimR
Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (18/6); total (18/7)
Fisher's exact test for biased strand distribution p-value = 2.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

AAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTGTGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAGTATCAGCTGTCCTTTGC  >  NC_000913/1875307‑1875461

aaacagaaaacagaGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATgg                                                                            >  1:343388/1‑81 (MQ=255)

    agaaaacagaGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATggcgg                                                                         >  1:343399/1‑80 (MQ=255)

           agagTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATcc                                                                 <  1:343364/81‑1 (MQ=255)

              gTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCcac                                                               >  2:343395/1‑80 (MQ=255)

                 cAGCATTAGCCGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACaaa                                                            <  1:343365/80‑1 (MQ=255)

                  aGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAg                                                           >  2:343387/1‑80 (MQ=255)

                   gCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCa                                                         <  2:343366/81‑1 (MQ=255)

                     aTTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCAtt                                                       >  2:343403/1‑81 (MQ=255)

                      ttAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCAttt                                                      >  1:343380/1‑81 (MQ=255)

                           tGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCAc                                                 >  2:343409/1‑81 (MQ=255)

                               aCTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTa                                             >  1:343402/1‑81 (MQ=255)

                                   gATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACa                                           <  1:343367/79‑1 (MQ=255)

                                   gATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAgg                                         >  1:343382/1‑81 (MQ=255)

                                          aTGTTCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTg                                   >  1:343406/1‑80 (MQ=255)

                                              tCCACCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCa                              >  2:343392/1‑81 (MQ=255)

                                                 aCCCCGCCCGGTATCCAAACCGCATATTGTGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGt                           <  1:343368/81‑1 (MQ=255)

                                                 aCCCCGCCCGGTATCCAAACCGCATATTATGGCGGCACCGTCCCCAAAGCTTTTTCCACCGTACAGGTAATTGCACCATGt                           <  2:343369/81‑1 (MQ=255)

                                                       cccgGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAgcgc                      >  2:343397/1‑80 (MQ=255)

                                                         cgGTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAg                   >  1:343398/1‑81 (MQ=255)

                                                           gTATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAGTa                 <  1:343370/81‑1 (MQ=255)

                                                            tATCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAGTAt                >  2:343401/1‑81 (MQ=255)

                                                             aTCCAAACCGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAGTAt                >  1:343405/1‑80 (MQ=255)

                                                                     cGCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAGTATCAGCTGTcc       >  2:343396/1‑81 (MQ=255)

                                                                      gCATATTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAGTATCAGCTGTCCt      >  2:343417/1‑81 (MQ=255)

                                                                          atTATGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAGTATCAGCTGTCCTTTGc  >  2:343412/1‑81 (MQ=255)

AAACAGAAAACAGAGTTCAGCATTAGCTGTTACTTGATTGCTATGTTCCACCCCGCCCGGTATCCAAACCGCATATTGTGGCGGCACCATCCACAAAGCATTTTCCACCGTACAGGTAATTGCACCATGTAGCGCCAGTATCAGCTGTCCTTTGC  >  NC_000913/1875307‑1875461

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A