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 F28 I1 R1	159	82.1	2830106	99.3%	2810295	139.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,443,320	C→T	A260T (GCA→ACA)	secY ←	Sec translocon subunit SecY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,443,320	0	C	T	100.0%	182.5 / NA	52	A260T (GCA→ACA)	secY	Sec translocon subunit SecY
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (28/24); total (28/24)

GTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACGAGGAAGTGCAGG  >  NC_000913/3443187‑3443456

gtCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATa                                                                                                                                    >  2:528942/1‑140 (MQ=255)

gtCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATa                                                                                                                                    >  1:321431/1‑140 (MQ=255)

              aCCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCtt                                                                                                                      >  2:1358584/1‑140 (MQ=255)

                   tACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGa                                                                                                                 >  1:193586/1‑140 (MQ=255)

                   tACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGa                                                                                                                 >  1:244784/1‑140 (MQ=255)

                        cccccGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGttt                                                                                                            >  1:1113063/1‑140 (MQ=255)

                        cccccGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGttt                                                                                                            >  1:335535/1‑140 (MQ=255)

                         ccccGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTc                                                                                                           >  1:414629/1‑140 (MQ=255)

                            caaaCCATGCCGCGATGGTCGCGGGAAACAAAATAATACGGGAAGGGAAGTTTGCGGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTcgcg                                                                                                        <  1:591761/138‑1 (MQ=255)

                            cGAACCATGACGGGAGGGCCGCGGAAAAAAAAATAATACTGGAAGCGAAGATGGCGGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTcgcg                                                                                                        <  2:1113063/140‑1 (MQ=255)

                                   tGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTa                                                                                                 >  1:516543/1‑140 (MQ=255)

                                   tGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTa                                                                                                 >  1:1095353/1‑140 (MQ=255)

                                   tGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTa                                                                                                 >  2:645690/1‑140 (MQ=255)

                                           tGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATg                                                                                         >  1:1240099/1‑140 (MQ=255)

                                           gggTTGCCGGGAAAAAAATAATGCTGGCAGCGATTATTGCCGGGACCCCCCCCGCCATATTCACTTTCAGCGGTGAATGTGTGCTCTGTGTAGCATAGACACGTCGACCTTGCTGCCGTTTCGAGTAGTTTACCACAATg                                                                                         <  2:1114958/139‑1 (MQ=255)

                                            ggccGCCGGAAAAAAAAAAATATGGGAAGCAAAGATGGCCGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATgc                                                                                        <  1:379199/137‑1 (MQ=255)

                                              tCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATgcgg                                                                                      >  1:1114958/1‑140 (MQ=255)

                                                     aaaCAAAATAATACGGGAAGCGAAGATGGCCGGGTTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGAc                                                                               <  2:1095353/139‑1 (MQ=255)

                                                          aaataatATGGAAAGAGAAGTTGGCGGGTATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGc                                                                          <  1:46178/139‑1 (MQ=255)

                                                            ataataCTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTc                                                                        >  1:1356917/1‑140 (MQ=255)

                                                             aaataCGGGAAGCGAAGATGGCCGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTca                                                                       <  1:559174/139‑1 (MQ=255)

                                                             aaataCGGGAAGAGAAGTTTGCGGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTca                                                                       <  1:422906/139‑1 (MQ=255)

                                                             aaaaggtGGAAGAGACGGTTGCGGGGTTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTca                                                                       <  2:601331/134‑1 (MQ=255)

                                                               ataCTGGAAGGGAAGATTGCGGGGATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaac                                                                     <  1:117343/140‑1 (MQ=255)

                                                               ataCTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaac                                                                     <  1:645690/140‑1 (MQ=255)

                                                               ataCTGGAAGAAAAGATGGCCGGTATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaac                                                                     <  2:1212631/140‑1 (MQ=255)

                                                                  cTGGAAGCGAAGATGGCGGGGTTCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACaaa                                                                  <  2:1240099/140‑1 (MQ=255)

                                                                     gAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATac                                                               >  1:601331/1‑140 (MQ=255)

                                                                     gAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATac                                                               >  2:166726/1‑140 (MQ=255)

                                                                     gAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATac                                                               >  2:60620/1‑140 (MQ=255)

                                                                       aGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGc                                                                          >  2:916838/1‑127 (MQ=255)

                                                                       aGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGc                                                                          <  1:916838/127‑1 (MQ=255)

                                                                         cGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATacctgt                                                           >  1:654262/1‑136 (MQ=255)

                                                                               ttGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaacaa                                                                   <  1:58482/126‑1 (MQ=255)

                                                                               ttGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaacaa                                                                   >  2:58482/1‑126 (MQ=255)

                                                                                 gCCGGAATCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGt                                                   <  1:181745/140‑1 (MQ=255)

                                                                                   gggtaTTCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCa                                                 <  1:896978/136‑1 (MQ=255)

                                                                                        ttccccccGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCa                                            <  2:1235297/137‑1 (MQ=255)

                                                                                        ttACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCa                                            <  2:193586/140‑1 (MQ=255)

                                                                                        ttACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCa                                            >  1:1278252/1‑140 (MQ=255)

                                                                                        ttACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCa                                            <  2:886684/140‑1 (MQ=255)

                                                                                             cccGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatac                                       <  1:528942/140‑1 (MQ=255)

                                                                                                gCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatactaa                                    >  2:911852/1‑140 (MQ=255)

                                                                                                     atTCACTTTCAGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTg                               <  2:710643/140‑1 (MQ=255)

                                                                                                               aGCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAg                     <  2:1094073/140‑1 (MQ=255)

                                                                                                                gCGGTAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGc                    >  2:964106/1‑140 (MQ=255)

                                                                                                                    tAAATGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAaca                <  1:911852/140‑1 (MQ=255)

                                                                                                                      aaTGTGTGCTCTGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACg              <  2:1356917/140‑1 (MQ=255)

                                                                                                                              ctctGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACGAGGAAGTg      >  1:623206/1‑140 (MQ=255)

                                                                                                                              ctctGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACGAGGAAGTg      >  2:1221736/1‑140 (MQ=255)

                                                                                                                              ctctGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACGAGGAAGTg      >  2:1187219/1‑140 (MQ=255)

                                                                                                                                ctGTGTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACGAGGAAGTGCa    >  1:92199/1‑140 (MQ=255)

                                                                                                                                 tgtgTAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACGAGGAAGTGCAg   >  2:1064017/1‑140 (MQ=255)

                                                                                                                                  gtgtAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACGAGGAAGTGCAgg  >  2:406645/1‑140 (MQ=255)

GTCAGCCAGTTCCAACCAGTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATTACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTAATACTGCAACCAACAGCAACACGAGGAAGTGCAGG  >  NC_000913/3443187‑3443456

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A