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
A4 F50 I2 R1	104	44.1	1376607	98.9%	1361464	150.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,954,322	T→C	L294P (CTG→CCG)	cmoB →	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,954,322	0	T	C	97.9%	150.4 / NA	47	L294P (CTG→CCG)	cmoB	tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (24/22); minor base G (0/1); total (24/23)
Fisher's exact test for biased strand distribution p-value = 4.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAATGCGTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAA  >  NC_000913/1954174‑1954465

cAAATGCGTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCgg                                                                                                                                               >  1:153006/1‑151 (MQ=255)

cAAATGCGTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCgg                                                                                                                                               <  2:325471/151‑1 (MQ=255)

 aaaTGCGTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGc                                                                                                                                              >  1:375801/1‑151 (MQ=255)

   aTGCGTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCgccggccg                                                                                                                                            >  1:172315/1‑151 (MQ=255)

    tGCGTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCgccggccg                                                                                                                                            >  1:204437/1‑150 (MQ=255)

       gTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGAttt                                                                                                                                        <  2:451059/151‑1 (MQ=255)

       gTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGAttt                                                                                                                                        >  1:55466/1‑151 (MQ=255)

          aTGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCt                                                                                                                                     <  2:42394/151‑1 (MQ=255)

                aTTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGAc                                                                                                                                 <  1:302698/149‑1 (MQ=255)

                 tttCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGAccc                                                                                                                               >  1:503481/1‑150 (MQ=255)

                       cccTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGa                                                                                                                         <  2:450145/150‑1 (MQ=255)

                       cccTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGAt                                                                                                                        >  1:250772/1‑151 (MQ=255)

                           tCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATcc                                                                                                                      <  1:191264/149‑1 (MQ=255)

                              gcgctggcgctgAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCACTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTa                                                                                                                 <  1:598721/151‑1 (MQ=255)

                                   ggcgctgAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTaaaa                                                                                                              <  2:401817/149‑1 (MQ=255)

                                   ggcgctgAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACg                                                                                                            <  1:246640/151‑1 (MQ=255)

                                       ctgAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTgg                                                                                                        >  2:646034/1‑151 (MQ=255)

                                             aaCTGGCTGAAGAAGCGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGtt                                                                                                  >  1:673768/1‑151 (MQ=255)

                                                  gCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCg                                                                                             >  2:443022/1‑151 (MQ=255)

                                                   cTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCgg                                                                                            >  1:174272/1‑151 (MQ=255)

                                                        gaagTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCt                                                                                       >  2:514453/1‑151 (MQ=255)

                                                            tgtgGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAAc                                                                                   >  2:192781/1‑151 (MQ=255)

                                                             gtgGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAAc                                                                                   <  2:288112/150‑1 (MQ=255)

                                                                gTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAAcgcgc                                                                               <  2:348763/151‑1 (MQ=255)

                                                                 ttttGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAAcgcgcg                                                                              >  1:451833/1‑151 (MQ=255)

                                                                    tGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGt                                                                            <  1:407756/150‑1 (MQ=255)

                                                                         atatCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGAt                                                                      >  2:85839/1‑151 (MQ=255)

                                                                              cGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTgcgc                                                                 >  1:647549/1‑151 (MQ=255)

                                                                               gCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTgcgcg                                                                >  1:522474/1‑151 (MQ=255)

                                                                                cATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTgcgcgc                                                               <  1:178444/151‑1 (MQ=255)

                                                                                 aTTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTgcgcgc                                                               >  1:164564/1‑150 (MQ=255)

                                                                                     cGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCAACGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGcc                                                          <  1:58729/151‑1 (MQ=255)

                                                                                                   accaccACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGt                                             >  2:434258/1‑150 (MQ=255)

                                                                                                    ccaccaCAGAAGAGCAGCGAGGCACCGAAGGGATGGTTCCCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGGGCTGATGGCGCGCAAGCCGTAAAGGTCTg                                               <  1:520303/147‑1 (MQ=255)

                                                                                                    ccaccaCAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCCCATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGt                                             <  1:29442/149‑1 (MQ=255)

                                                                                                        cacaGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACt                                       >  2:592341/1‑151 (MQ=255)

                                                                                                           tgaagaGGAGCGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATTATCCGGGTAAAACGGTGGCAGGTTATCTGGCACCTAAACGCGCGGTGCTGATTGCCCGCAAGCCGGAAAGGCATGGTATTACTGcc                                    >  1:681009/2‑151 (MQ=255)

                                                                                                                    gcGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATgc                              <  1:513918/148‑1 (MQ=255)

                                                                                                                     cGACGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCGGGGTAAACCGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATgcggc                           <  1:612335/150‑1 (MQ=255)

                                                                                                                        cGCACCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGGGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTg                        <  1:180373/150‑1 (MQ=255)

                                                                                                                           aCCGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAATCGGTGGAAGGTTATCCGGCACCTAAACGCGCGGGGCTGATTGCGCGCAAGCCGTAAAGGTCCGGTATTACTGCCGGATGCCGCGTGCAc                     >  1:515859/1‑150 (MQ=255)

                                                                                                                             cGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGcc                  >  2:590129/1‑151 (MQ=255)

                                                                                                                             cGAATGGATGGTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGcc                  >  2:580493/1‑151 (MQ=255)

                                                                                                                                     tggTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCgg          >  2:476446/1‑151 (MQ=255)

                                                                                                                                      ggTTACCGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGc         >  1:147879/1‑151 (MQ=255)

                                                                                                                                           ccGAATCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACa    <  2:204440/151‑1 (MQ=255)

                                                                                                                                            cGAATCGCGGGCCGATTTCCTCGACCCACATGGTCGGGGTAAAGCGGGGAAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGAAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACaa   <  1:424545/151‑1 (MQ=38)

                                                                                                                                            cGAATCGCCGGCCGATTCCCCCGACCCACAGGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGGGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACaa   <  1:493742/151‑1 (MQ=255)

                                                                                                                                              aaTCGCCGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACaaa  <  2:552979/150‑1 (MQ=255)

CAAATGCGTAATGTCTATTTCATCCCTTCCGCGCTGGCGCTGAAAAACTGGCTGAAGAAGTGTGGTTTTGTAGATATCCGCATTGCGGATGTGAGCGTTACCACCACAGAAGAGCAGCGACGCACCGAATGGATGGTTACCGAATCGCTGGCCGATTTCCTCGACCCACATGATCCGGGTAAAACGGTGGAAGGTTATCCGGCACCTAAACGCGCGGTGCTGATTGCGCGCAAGCCGTAAAGGTCTGGTATTACTGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACAAA  >  NC_000913/1954174‑1954465

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A