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
A10 F1 I1 R1	77	35.1	1569012	96.6%	1515665	112.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,595,427	A→G	pseudogene (2561/3861 nt)	yneO ←	pseudogene, AidA homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,595,427	0	A	G	100.0%	136.2 / NA	36	pseudogene (2561/3861 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (11/25); total (11/25)

TTTGCGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTACCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGCCAGTC  >  NC_000913/1595293‑1595562

tttGCGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTg                                                                                                                                     >  2:537398/1‑139 (MQ=255)

  tGCGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGAt                                                                                                                                   >  1:710286/1‑139 (MQ=255)

        ttCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTAc                                                                                                                             <  2:5682/139‑1 (MQ=255)

        ttCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTAc                                                                                                                             >  2:6871/1‑139 (MQ=255)

           aCCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGc                                                                                                                          <  1:249616/139‑1 (MQ=255)

           aCCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGc                                                                                                                          <  1:281077/139‑1 (MQ=255)

            ccAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGcc                                                                                                                         <  2:301021/139‑1 (MQ=255)

                ttGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTc                                                                                                                     <  2:763054/139‑1 (MQ=255)

                     cGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGgt                                                                                                                <  1:6871/139‑1 (MQ=255)

                                    cgtcgtGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGcc                                                                                                 >  2:156824/1‑139 (MQ=255)

                                        gtgtTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACa                                                                                             >  2:319244/1‑139 (MQ=255)

                                          gtTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAAc                                                                                           <  1:319244/139‑1 (MQ=255)

                                                      tGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGAc                                                                               <  2:457272/139‑1 (MQ=255)

                                                       gAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACg                                                                              <  2:710286/139‑1 (MQ=255)

                                                       gAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACg                                                                              <  2:150428/139‑1 (MQ=255)

                                                        aGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGc                                                                             <  2:689008/139‑1 (MQ=255)

                                                        aGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGc                                                                             <  2:484573/139‑1 (MQ=255)

                                                                         aTTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCcgcg                                                            >  2:6922/1‑139 (MQ=255)

                                                                          ttCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGa                                                           >  1:145257/1‑139 (MQ=255)

                                                                           tCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAg                                                          <  2:544026/139‑1 (MQ=255)

                                                                               cATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTc                                                      <  2:719832/139‑1 (MQ=255)

                                                                                  gggATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCgca                                                   <  1:156824/139‑1 (MQ=255)

                                                                                        aTTCCACGGTTTAGGCACGTCGATATGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCtttg                                                                                                                     <  1:481237/67‑2 (MQ=255)

                                                                                        aTTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTc                                                                                                                     >  2:481237/1‑67 (MQ=255)

                                                                                        aTTACACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGa                                             >  2:504896/1‑139 (MQ=255)

                                                                                         ttCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGcc                                                                                                                         >  2:173211/1‑62 (MQ=255)

                                                                                         ttCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGcc                                                                                                                         <  1:173211/62‑1 (MQ=255)

                                                                                                           tCGATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAatga                          >  2:328515/1‑139 (MQ=255)

                                                                                                             gATAAGCACGTCGCCCGTCCCGTTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAatgatg                        <  1:328515/139‑1 (MQ=255)

                                                                                                                              tcccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGc       <  1:112653/139‑1 (MQ=255)

                                                                                                                              tcccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGc       <  2:676644/139‑1 (MQ=255)

                                                                                                                              tcccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGc       <  1:537398/139‑1 (MQ=255)

                                                                                                                              tcccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGc       <  1:673377/139‑1 (MQ=255)

                                                                                                                              tcccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGc       <  2:145257/139‑1 (MQ=255)

                                                                                                                              tcccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGc       <  2:219487/139‑1 (MQ=255)

                                                                                                                               cccgtTTGCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGcc      <  2:23905/139‑1 (MQ=255)

                                                                                                                                   ttttCCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGCCAGTc  <  1:504896/139‑1 (MQ=255)

TTTGCGCCTTCACCAGTTGAACGCCGACATGGCTATCGTCGTGTTCCAGCAAATTGAGCGTCGTCAGAGGGTTATTCGCCATGGGATCATTCCACGGTTTAGGCACGTCGATAAGCACGTCGCCCGTCCCGTTTACCTGATAGTTACGGCCTTTCCAGGTGTAGTCACCCGCGCCGACAACCAGCGTATCGACGCTGATATATCCCTCCGCGAGCGTCGCAGCAGGAATATCCGTATCGAAAATGATGGTACCTCCATTCATGGCCAGTC  >  NC_000913/1595293‑1595562

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A