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
A5 F1 I1 R1	770	51.4	2439994	93.8%	2288714	110.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,958,496	G→A	intergenic (‑364/+24)	torY ← / ← cutC	TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,958,496	0	G	A	100.0%	203.1 / NA	64	intergenic (‑364/+24)	torY/cutC	TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (35/29); total (35/29)

TATTTTTAGCACAACGCTATGCGCACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGGGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGACAATCC  >  NC_000913/1958360‑1958630

tatTTTTAGCACAACGCTATGCGCACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCACTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGc                                                                                                                                      >  2:493172/1‑139 (MQ=255)

                   tGCGCACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTaaa                                                                                                                   >  2:664850/1‑139 (MQ=255)

                      gcACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAAt                                                                                                                >  1:869322/1‑139 (MQ=255)

                        aCTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCa                                                                                                              >  1:249363/1‑139 (MQ=255)

                          tGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCAtt                                                                                                            >  1:1189184/1‑139 (MQ=255)

                          tGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCAtt                                                                                                            >  2:173399/1‑139 (MQ=255)

                               cccGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGcc                                                                                                       <  2:1189184/139‑1 (MQ=255)

                                     cAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATgg                                                                                                 <  2:249363/139‑1 (MQ=255)

                                                        ttcgttTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtttca                                                                              >  2:1094903/1‑139 (MQ=255)

                                                            ttttttATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAAc                                                                                                                         <  2:936509/92‑1 (MQ=255)

                                                            ttttttATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAAc                                                                                                                         >  1:936509/1‑92 (MQ=255)

                                                               tttATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGc                                                                       <  1:854342/139‑1 (MQ=255)

                                                                       gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGa                                                                                       <  2:912833/115‑1 (MQ=255)

                                                                       gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGa                                                                                       >  1:912833/1‑115 (MQ=255)

                                                                       gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAAccgccg                                                               >  2:1202885/1‑139 (MQ=255)

                                                                       gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAAccgccg                                                               <  1:739116/139‑1 (MQ=255)

                                                                       gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAAccgccg                                                               >  1:894030/1‑139 (MQ=255)

                                                                       gTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAAccgccg                                                               >  1:1054525/1‑139 (MQ=255)

                                                                        ttCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCaa                                                                                          >  1:1052134/1‑111 (MQ=255)

                                                                        ttCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCaa                                                                                          <  2:1052134/111‑1 (MQ=255)

                                                                        ttCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACcgccgc                                                              >  2:788349/1‑139 (MQ=255)

                                                                        ttCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACcgccgc                                                              >  2:227755/1‑139 (MQ=255)

                                                                         tCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             <  1:664850/139‑1 (MQ=255)

                                                                           aGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGGTTCCTTTCATTTCAGCAACCGCCGcccc                                                           <  2:869322/139‑1 (MQ=255)

                                                                           aGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGcccc                                                           <  1:493172/139‑1 (MQ=255)

                                                                           aGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGcccc                                                           <  1:173399/139‑1 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAAc                                                                                                                         >  1:1088257/1‑70 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAAc                                                                                                                         <  2:1088257/70‑1 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGAt                                                                                                   >  1:1138329/1‑92 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGAt                                                                                                   <  2:1138329/92‑1 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCg                                                                                               >  1:77528/1‑96 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCg                                                                                               <  2:77528/96‑1 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGc                                                                       <  2:972990/120‑1 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGc                                                                       >  1:972990/1‑120 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAATCGCCGCCCCGTCTACg                                                    >  1:46858/1‑139 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACg                                                    >  2:707484/1‑139 (MQ=255)

                                                                                  aaaaaaGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACg                                                    >  2:180719/1‑139 (MQ=255)

                                                                                       aGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             >  1:476424/1‑125 (MQ=255)

                                                                                       aGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             <  2:476424/125‑1 (MQ=255)

                                                                                           cccTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAAcgc                                           <  1:1094903/139‑1 (MQ=255)

                                                                                                         cAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGatat                                                <  2:627834/120‑1 (MQ=255)

                                                                                                         cAGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGatat                                                >  1:627834/1‑120 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCg                                                                                               >  2:645406/1‑72 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCg                                                                                               <  1:645406/72‑1 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtt                                                                                 >  2:108896/1‑86 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtt                                                                                 >  1:355045/1‑86 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtt                                                                                 <  1:108896/86‑1 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCtt                                                                                 <  2:355045/86‑1 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             >  2:700077/1‑106 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             <  1:700077/106‑1 (MQ=255)

                                                                                                          aGGGGCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCAATTGGCCTGATAGGGTTCAATGGTTCCTTTCATTTCAGCAACCGCCGCCCCGCCTACGATATAACGCGAATACTCGTCcgcg                            >  1:916227/1‑139 (MQ=255)

                                                                                                              gCCTGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGtt                        <  2:894030/139‑1 (MQ=255)

                                                                                                                 tGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCaa                                                                                          <  2:269559/70‑1 (MQ=255)

                                                                                                                 tGGTACGAGCAAGCATCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCaa                                                                                          >  1:269559/1‑70 (MQ=255)

                                                                                                                        agcaagcaTCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             >  1:6260/1‑92 (MQ=255)

                                                                                                                        agcaagcaTCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCgccgcc                                                             <  2:6260/92‑1 (MQ=255)

                                                                                                                        agcaagcaTCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCtgatga              >  2:318704/1‑139 (MQ=255)

                                                                                                                        agcaagcaTCATATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCACTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCtgatga              >  2:734220/1‑139 (MQ=255)

                                                                                                                            agcaTCATATTGAGCGACATGATGCAACGGTaaaa                                                                                                                  >  2:282781/1‑35 (MQ=255)

                                                                                                                            agcaTCATATTGAGCGACATGATGCAACGGTaaaa                                                                                                                  <  1:282781/35‑1 (MQ=255)

                                                                                                                              catcatATTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGa        <  1:734220/139‑1 (MQ=255)

                                                                                                                                   tatTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGACAATc   >  2:661146/1‑139 (MQ=255)

                                                                                                                                    atTGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATTATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGACAATcc  <  1:227755/139‑1 (MQ=255)

                                                                                                                                     ttGAGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGa        <  1:669333/132‑1 (MQ=255)

TATTTTTAGCACAACGCTATGCGCACTGTCACCCGCTCAACAGATCACGGTTATCGTTCGTTTTTTATACTGTTCAGGGATAAAAAAAGGCCCCTGTTGAAATTGCAGGGGCCTGGTACGAGCAAGCATCATATTGGGCGACATGATGCAACGGTAAAAATCATTTGGCCTGATGGCGTTCAATGATTCCTTTCATTTCAGCAACCGCCGCCCCGTCTACGATATAACGCGAATACTCGTCCGCGTGTTCATCTGATGACATGGACAATCC  >  NC_000913/1958360‑1958630

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A