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	1,874,640	C→A	31.6%	R87R (CGG→CGT)	ygcF ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,874,640	0	C	A	31.6%	77.7 / 36.1	63	R87R (CGG→CGT)	ygcF	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (23/20); new base A (14/6); total (37/26)
Fisher's exact test for biased strand distribution p-value = 2.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

CAGTCAGTGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTCACTGCTCGCAGCCCCCCACTTA  >  minE/1874585‑1874706

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:106989/1‑69 (MQ=255)

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:704979/1‑69 (MQ=255)

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:447072/1‑69 (MQ=255)

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:3162173/1‑69 (MQ=255)

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:3151772/1‑69 (MQ=255)

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:271719/1‑69 (MQ=255)

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:2144566/1‑69 (MQ=255)

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:1976760/1‑69 (MQ=255)

cagtcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATc                                                       >  1:1933853/1‑69 (MQ=255)

   tcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCt                                                    >  1:949903/1‑69 (MQ=255)

   tcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCt                                                    >  1:795848/1‑69 (MQ=255)

   tcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCt                                                    >  1:2951379/1‑69 (MQ=255)

   tcagtGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCt                                                    >  1:2152922/1‑69 (MQ=255)

         gcagcaAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCg                                                >  1:602503/1‑67 (MQ=255)

         gcagcaAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGa                                               >  1:1643269/1‑68 (MQ=255)

         gcagcaAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGa                                               >  1:396138/1‑68 (MQ=255)

         gcagcaAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGa                                               >  1:561879/1‑68 (MQ=255)

             caAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAAt                                          <  1:2138262/69‑1 (MQ=255)

               aaTCATGAATGCAAGGCTCACCACCCGTAATCACCACATGACGCGCGGTGTATCCCTGACGGCCAATGa                                        <  1:1272269/69‑1 (MQ=255)

               aaTCATGAATGCAAGGCTCACCACCCGTAATCACCACATGACGCGCGGTGTATCCCTGACGGCCAATGa                                        <  1:895232/69‑1 (MQ=255)

               aaTCATGAATGCAAGGCTCACCACCCGTAATCACCACATGACGCGCGGTGTATCCCTGACGGCCAATGa                                        <  1:1236407/69‑1 (MQ=255)

               aaTCATGAATGCAAGGCTCACCACCCGTAATCACCACATGACGCGCGGTGTATCCCTGACGGCCAATGa                                        <  1:2028702/69‑1 (MQ=255)

               aaTCATGAATGCAAGGCTCACCACCCGTAATCACCACATGACGCGCGGTGTATCCCTGACGGCCAATGa                                        <  1:1606259/69‑1 (MQ=255)

                aTCATGAATGCAAGGCTCACCACCCGTAATCACCACATGACGCGCGGTGTATCCCTGACGGCCAATGa                                        <  1:1931490/68‑1 (MQ=255)

                   aTGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGaaa                                      >  1:611790/1‑65 (MQ=255)

                   aTGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGAca                                      >  1:1615310/1‑67 (MQ=255)

                   aTGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGAca                                      >  1:1216268/1‑67 (MQ=255)

                   aTGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGAca                                      >  1:2993280/1‑67 (MQ=255)

                        tGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCa                               <  1:2152122/69‑1 (MQ=255)

                        tGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCa                               <  1:1459656/69‑1 (MQ=255)

                        tGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCa                               <  1:2529125/69‑1 (MQ=255)

                        tGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCa                               <  1:605000/69‑1 (MQ=255)

                        tGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCa                               <  1:1772166/69‑1 (MQ=255)

                        tGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCa                               <  1:1704249/69‑1 (MQ=255)

                         gCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCa                               <  1:2570068/68‑1 (MQ=255)

                            aGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATc                           <  1:877618/69‑1 (MQ=255)

                               cTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTc                        <  1:2623337/69‑1 (MQ=255)

                               cTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTc                        <  1:2946219/69‑1 (MQ=255)

                               cTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTc                        <  1:1844686/69‑1 (MQ=255)

                               cTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTc                        <  1:1728858/69‑1 (MQ=255)

                               cTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTc                        <  1:3194171/69‑1 (MQ=255)

                               cTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTc                        <  1:363965/69‑1 (MQ=255)

                               cTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTc                        <  1:338510/69‑1 (MQ=255)

                                               accacATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTCACTGCTCGCAGccccc        >  1:1514705/1‑69 (MQ=255)

                                               accacATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTCACTGCTCGCAGccccc        >  1:1380270/1‑69 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCtt                         >  1:1575527/1‑51 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:1067383/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:1195847/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:3247514/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:3237963/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:3055221/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:1486934/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:255814/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:2400786/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:210558/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:1853926/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:1765361/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:1757782/1‑57 (MQ=255)

                                                ccacATGACGCGCGGTGTATCCCTGACGGCCAATGACAGCCAGCAAATCTTCACTGc                   >  1:1679283/1‑57 (MQ=255)

                                                     tGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTCACTGCTCGCAGCCCCCCACTTa  <  1:3389335/69‑1 (MQ=255)

                                                     tGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTCACTGCTCGCAGCCCCCCACTTa  <  1:318513/69‑1 (MQ=255)

                                                     tGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTCACTGCTCGCAGCCCCCCACTTa  <  1:601445/69‑1 (MQ=255)

                                                     tGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTCACTGCTCGCAGCCCCCCACTTa  <  1:2093395/69‑1 (MQ=255)

CAGTCAGTGGCAGCAAATCATGAATGCAAGGCTCACCACCCGTAATCACCACATGCCGCGCGGTGTATCCCTGGCGACCAATGACAGCCAGCAAATCTTCACTGCTCGCAGCCCCCCACTTA  >  minE/1874585‑1874706

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A