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	2,924,094	T→C	34.5%	P376P (CCA→CCG)	valS ←	valyl‑tRNA synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,924,094	0	T	C	34.5%	33.5 / 26.5	52	P376P (CCA→CCG)	valS	valyl‑tRNA synthetase
Reads supporting (aligned to +/- strand): ref base T (15/19); new base C (8/10); total (23/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAACCGCTTCAACCGCCGGTTTCGCCAGGACATCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTCC  >  minE/2924030‑2924160

cAACCGCTTCAACCGCTGGTTTCGCCAGTACATCGGCACGAACGTACCACTGGTCGGTCAGCATCGGt                                                                 >  1:1034544/1‑68 (MQ=255)

cAACCGCTTCAACCGCTGGTTTCGCCAGTACATCGGCACGAACGTACCACTGGTCGGTCAGCATCGGt                                                                 >  1:275445/1‑68 (MQ=255)

cAACCGCTTCAACCGCTGGTTTCGCCAGTACATCGGCACGAACGTACCACTGGTCGGTCAGCATCGGt                                                                 >  1:2776339/1‑68 (MQ=255)

cAACCGCTTCAACCGCTGGTTTCGCCAGTACATCGGCACGAACGTACCACTGGTCGGTCAGCATCGGt                                                                 >  1:1440670/1‑68 (MQ=255)

cAACCGCTTCAACCGCTGGTTTCGCCAGTACATCGGCACGAACGTACCACTGGTCGGTCAGCATCGGt                                                                 >  1:4324/1‑68 (MQ=255)

cAACCGCTTCAACCGCTGGTTTCGCCAGTACATCGGCACGAACGTACCACTGGTCGGTCAGCATCGGt                                                                 >  1:54555/1‑68 (MQ=255)

cAACCGCTTCAACCGCTGGTTTCGCCAGTACATCGGCACGAACGTACCACTGGTCGGTCAGCATCGGt                                                                 >  1:85168/1‑68 (MQ=255)

cAACCGCTTCAACCGCTGGTTTCGCCAGTACATCGGCACGAACGTACCACTGGTCGGTCAGCATCGGt                                                                 >  1:1137977/1‑68 (MQ=255)

   ccGCTTCAACCGCCGGTTTCGCCAGGACATCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTc                                                               <  1:1290732/67‑1 (MQ=255)

   ccGCTTCAACCGCCGGTTTCGCCAGGACATCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTc                                                               <  1:3237872/67‑1 (MQ=255)

   ccGCTTCAACCGCCGGTTTCGCCAGGACATCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTc                                                               <  1:1824004/67‑1 (MQ=255)

   ccGCTTCAACCGCCGGTTTCGCCAGGACATCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTc                                                               <  1:2410558/67‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:625015/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:334706/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:2796985/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:112866/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:2552674/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:254373/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:2258308/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:222647/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:1142938/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:1925550/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:1183402/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:1894004/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:139253/69‑1 (MQ=255)

                               aTCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgg                                 <  1:1479519/69‑1 (MQ=255)

                                  ggCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAAc                              >  1:60302/1‑69 (MQ=255)

                                                   ggtcggtcAGCATTGGTTCGATAACTACGCCGCCACGTTCGCCGTAAGGAACGGTCAGGTCGTGCGGt              >  1:2416167/1‑68 (MQ=255)

                                                   ggtcggtcAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGt              >  1:26290/1‑68 (MQ=255)

                                                   ggtcggtcAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGt              >  1:36171/1‑68 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:2144102/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:819178/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:818990/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:678978/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:619738/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:1286850/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:2787076/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:233555/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:1921847/69‑3 (MQ=255)

                                                      cggtcAGCATCGGTTCGATAACCACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGtttga          <  1:2144514/69‑3 (MQ=255)

                                                       ggtcAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAgt                                 <  1:1426329/45‑2 (MQ=255)

                                                          cAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATttc      >  1:2915539/1‑69 (MQ=255)

                                                          cAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATttc      >  1:763915/1‑69 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGt              >  1:3285808/1‑57 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTcc  >  1:2804768/1‑69 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTcc  >  1:1803356/1‑69 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTcc  >  1:1843539/1‑69 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTcc  >  1:1222512/1‑69 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTcc  >  1:1847479/1‑69 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTcc  >  1:1909165/1‑69 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTcc  >  1:2346102/1‑69 (MQ=255)

                                                              aTTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTcc  >  1:1955286/1‑69 (MQ=255)

CAACCGCTTCAACCGCCGGTTTCGCCAGGACATCGGCACGCACGTACCACTGGTCGGTCAGCATTGGTTCGATAACTACGCCGCCACGGTCGCCGTAAGGAACGGTCAGGTCGTGCGGTTTAATTTCTTCC  >  minE/2924030‑2924160

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