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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,599,311	C→T	58.2%	P279P (CCG→CCA)	yhiR ←	predicted DNA (exogenous) processing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,599,311	0	C	T	58.2%	14.8 / 38.9	55	P279P (CCG→CCA)	yhiR	predicted DNA (exogenous) processing protein
Reads supporting (aligned to +/- strand): ref base C (17/6); new base T (11/21); total (28/27)
Fisher's exact test for biased strand distribution p-value = 6.02e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCGCGATTGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGCCAC  >  minE/2599258‑2599374

aCCGCGATTGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCtt                                                  >  1:1633340/1‑69 (MQ=255)

aCCGCGATTGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCtt                                                  >  1:875294/1‑69 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:2292244/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:2342791/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:2516306/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:2093586/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:2011386/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:2621682/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:2755032/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:43919/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:538514/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:1618138/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:936731/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:1482522/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:963697/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:1110278/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:1222081/69‑1 (MQ=255)

        tGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:1132811/69‑1 (MQ=255)

        tGTAGCGAGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:98147/69‑1 (MQ=255)

         gTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCAGGATCCAGCTTACGGTGGc                                          <  1:892393/68‑1 (MQ=255)

         gTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:1449926/68‑1 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:2252150/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:2219535/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:2201954/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:764197/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:2514524/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:2131912/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:59452/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:1866173/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:3389827/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:300936/1‑69 (MQ=255)

                gagaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGCGTGCCCgg                                  >  1:2899813/1‑69 (MQ=255)

                 agaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGt                                 <  1:1667293/69‑1 (MQ=255)

                  gaCGTAATAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGt                                 <  1:1810355/68‑1 (MQ=255)

                        aTAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATcc                                                       >  1:1395915/1‑40 (MQ=255)

                        aTAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGtgcctgc                           >  1:1821944/1‑68 (MQ=255)

                        aTAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGtgcctgc                           >  1:1710121/1‑68 (MQ=255)

                        aTAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGtccctgc                           >  1:2333928/1‑68 (MQ=255)

                              gCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGtgcctgc                           >  1:2195047/1‑62 (MQ=255)

                              gCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAAcc                    >  1:3209276/1‑69 (MQ=255)

                              gCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAAcc                    >  1:3383328/1‑69 (MQ=255)

                              gCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAAcc                    >  1:464436/1‑69 (MQ=255)

                              gCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAAcc                    >  1:791318/1‑69 (MQ=255)

                              gCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAAcc                    >  1:2358628/1‑69 (MQ=255)

                              gCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTG‑CCGGTGCCTGCCGGAACCa                   >  1:796209/1‑69 (MQ=255)

                                     aTGGCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:3367522/40‑1 (MQ=255)

                                        gCTGCAATTACTCTGGCACGATCCAGCTTACGGTGGc                                          <  1:2254700/37‑1 (MQ=255)

                                              aTTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGc     <  1:3139810/68‑1 (MQ=255)

                                              aTTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGc     <  1:970186/68‑1 (MQ=255)

                                              aTTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGc     <  1:820785/68‑1 (MQ=255)

                                               ttACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGc     <  1:2604652/67‑1 (MQ=255)

                                                 aCTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGCCAc  >  1:2462522/1‑68 (MQ=255)

                                                 aCTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGCCAc  >  1:1576033/1‑68 (MQ=255)

                                                 aCTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGCCAc  >  1:2529265/1‑68 (MQ=255)

                                                 aCTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGCCAc  >  1:288406/1‑68 (MQ=255)

ACCGCGATTGTAGCGCGAGACGTAATAGGTGCCAGCAATGGCTGCAATTACTCCGGCACGATCCAGCTTACGGTGGCGTGCCCGGTGCCTGCCGGAACCAGTTTGCTGTGCAGCCAC  >  minE/2599258‑2599374

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