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	676,579	A→T	42.5%	A58A (GCT→GCA)	ompA ←	outer membrane protein A (3a;II*;G;d)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	676,579	0	A	T	42.5%	36.4 / 87.6	87	A58A (GCT→GCA)	ompA	outer membrane protein A (3a;II*;G;d)
Reads supporting (aligned to +/- strand): ref base A (15/35); new base T (15/22); total (30/57)
Fisher's exact test for biased strand distribution p-value = 3.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.98e-01

CGACCTAACCAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAGTGTCATGG  >  minE/676511‑676636

cGACCTAACCAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCa                                                            >  1:2749407/1‑69 (MQ=255)

cGACCTAACCAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCa                                                            >  1:2648827/1‑69 (MQ=255)

cGACCTAACCAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCa                                                            >  1:542037/1‑69 (MQ=255)

cGACCTAACCAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCa                                                            >  1:637523/1‑69 (MQ=255)

cGACCTAACCAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCa                                                            >  1:195350/1‑69 (MQ=255)

     tAACCAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAgcg                                                         >  1:3340944/1‑67 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAg                                                    >  1:2034601/1‑68 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:3231461/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:2932948/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:2907620/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:2896776/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:2841507/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:220052/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:749057/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:1790136/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:1769811/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:1100410/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:1403015/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:809132/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:1302960/1‑69 (MQ=255)

         cAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGt                                                   >  1:1310969/1‑69 (MQ=255)

             cGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑t                                              >  1:2035877/1‑69 (MQ=255)

             cGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑t                                              >  1:846972/1‑69 (MQ=255)

                aaCCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑tttt                                           <  1:79619/69‑1 (MQ=255)

                aaCCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑tttt                                           <  1:1851496/69‑1 (MQ=255)

                aaCCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑tttt                                           <  1:1921744/69‑1 (MQ=255)

                aaCCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑tttt                                           <  1:1679099/69‑1 (MQ=255)

                 aCCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑tttt                                           <  1:2094238/68‑1 (MQ=255)

                 aCCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑tttt                                           <  1:1908065/68‑1 (MQ=255)

                 aCCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTc                                          >  1:3236695/1‑69 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:3013130/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:3005944/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1387688/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:698466/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:2117824/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1154126/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1395701/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:69934/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:3048548/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:765378/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1899187/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1888692/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1827175/69‑3 (MQ=255)

                   ccATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1719681/69‑3 (MQ=255)

                    cATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:3061051/68‑3 (MQ=255)

                    cATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1866287/68‑3 (MQ=255)

                    cATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:3360547/68‑3 (MQ=255)

                    cATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:3065040/68‑3 (MQ=255)

                    cATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1165146/68‑3 (MQ=255)

                    cATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:1690918/68‑3 (MQ=255)

                        tCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTc                                   >  1:2313360/1‑69 (MQ=255)

                        tCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTc                                   >  1:303273/1‑69 (MQ=255)

                        tCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTc                                   >  1:383865/1‑69 (MQ=255)

                        tCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTc                                   >  1:1487613/1‑69 (MQ=255)

                        tCAAAGACAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTc                                   >  1:4395/1‑69 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCAttgttgtt                     <  1:3192789/69‑1 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCAttgttgtt                     <  1:2996575/69‑1 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCAttgttgtt                     >  1:515383/1‑69 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCAttgttgtt                     >  1:952881/1‑69 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCAttgttgtt                     >  1:1397097/1‑69 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCAttgttgtt                     <  1:1898340/69‑1 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCAttgttgtt                     >  1:3116482/1‑69 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCAttgttgtt                     <  1:1032542/69‑1 (MQ=255)

                                      cGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATAGGTCGGGCCAttgttgtt                     <  1:2507194/69‑1 (MQ=255)

                                           tAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTtgatga                <  1:2003673/69‑1 (MQ=255)

                                           tAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTtgatga                <  1:1793834/69‑1 (MQ=255)

                                           tAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTtgatga                <  1:2862663/69‑1 (MQ=255)

                                             aCCTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:2916479/43‑3 (MQ=255)

                                              ccTGGTAACCACCAAAAGCACCTGCACCCAGTTGG‑TTTTcgt                                        <  1:2563118/42‑3 (MQ=255)

                                               cTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAAcc            <  1:103237/69‑1 (MQ=255)

                                               cTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAAcc            <  1:2866599/69‑1 (MQ=255)

                                               cTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAAcc            <  1:3087038/69‑1 (MQ=255)

                                               cTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAAcc            <  1:116053/69‑1 (MQ=255)

                                               cTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGGCGGGCCATTGTTGTTGATGAAAcc            <  1:1207649/69‑1 (MQ=255)

                                                tGGTAACCACCAAAAGCACCAGCGCCCAGTTGGTTTTTCATGGGTCGGGCCATTGTTGTTGATGAAAcc            >  1:2213659/1‑69 (MQ=255)

                                                tGGTAACCACCAAAAGCA‑CAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAg          <  1:1904658/69‑1 (MQ=255)

                                                 ggTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAg          <  1:3433079/69‑1 (MQ=255)

                                                 ggTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAg          <  1:3268724/69‑1 (MQ=255)

                                                 ggTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAg          <  1:3222272/69‑1 (MQ=255)

                                                 ggTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAg          <  1:2145526/69‑1 (MQ=255)

                                                 ggTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAg          <  1:1407387/69‑1 (MQ=255)

                                                 ggTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGACATTGTTGTTGATGAAACCAg          <  1:372351/69‑1 (MQ=255)

                                                 ggTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGGCGGGCCATTGTTGTTGATGAAACCAg          <  1:2513864/69‑1 (MQ=255)

                                                 ggTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGGCGGGCCATTGTTGTTGATGAAACCAg          <  1:1929973/69‑1 (MQ=255)

                                                    aaCCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACTAgtgt       <  1:2483159/69‑1 (MQ=255)

                                                    aaCCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAgtgt       <  1:2102136/69‑1 (MQ=255)

                                                       caccaAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAGTGTCa     >  1:2936598/1‑68 (MQ=255)

                                                       caccaAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAGTGTCAt    <  1:117931/69‑1 (MQ=255)

                                                       caccaAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAGTGTCAt    <  1:975944/69‑1 (MQ=255)

                                                         ccaAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAGTGTCATgg  <  1:3431460/69‑1 (MQ=255)

                                                         ccaAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAGTGTCATgg  <  1:3389133/69‑1 (MQ=255)

                                                         ccaAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAGTGTCATgg  <  1:3161152/69‑1 (MQ=255)

CGACCTAACCAGTCGTAACCCATTTCAAAGCCAACATACGGGTTAACCTGGTAACCACCAAAAGCACCAGCGCCCAGTTGG‑TTTTCATGGGTCGGGCCATTGTTGTTGATGAAACCAGTGTCATGG  >  minE/676511‑676636

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