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
A12 F1 I1 R1	760	58.2	3022526	90.8%	2744453	102.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,129,581	G→A	pseudogene (563/1101 nt)	yghO ←	pseudogene, IS‑interrupted

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,129,581	0	G	A	100.0%	168.1 / NA	52	pseudogene (563/1101 nt)	yghO	pseudogene, IS‑interrupted
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (23/29); total (23/29)

GATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGC  >  NC_000913/3129450‑3129705

gATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCtt                                                                                                                       >  1:510129/1‑139 (MQ=255)

 aTCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttt                                                                                                                      >  2:71746/1‑139 (MQ=255)

    gCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTg                                                                                                                   <  1:806434/139‑1 (MQ=255)

      ccATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgcg                                                                                                                 <  2:905347/139‑1 (MQ=255)

        aTGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCa                                                                                                               <  2:1189570/139‑1 (MQ=255)

                gAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATcc                                                                                                       >  2:666962/1‑139 (MQ=255)

                    tCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCa                                                                                                   <  2:60832/139‑1 (MQ=255)

                              tAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAg                                                                                         >  2:1309645/1‑139 (MQ=255)

                                 aCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                                                      <  2:475385/139‑1 (MQ=255)

                                 aCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                                                      >  2:1135253/1‑139 (MQ=255)

                                   ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                    <  2:1386965/139‑1 (MQ=255)

                                   ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                    >  1:607259/1‑139 (MQ=255)

                                   ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                    <  1:1309645/139‑1 (MQ=255)

                                     cacaAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGga                                                                                  >  1:85300/1‑139 (MQ=255)

                                       caAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                <  1:71746/139‑1 (MQ=255)

                                                    gtgCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgag                                                                                 >  2:70273/1‑125 (MQ=255)

                                                    gtgCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgag                                                                                 <  1:70273/125‑1 (MQ=255)

                                                         gccagccaGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCg                                                              <  1:1135253/139‑1 (MQ=255)

                                                         gccagccaGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCg                                                              <  2:510129/139‑1 (MQ=255)

                                                            agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTa                                                                                          <  1:1232493/108‑1 (MQ=255)

                                                            agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTa                                                                                          >  2:1232493/1‑108 (MQ=255)

                                                            agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTg                                                           >  1:713369/1‑139 (MQ=255)

                                                                      gAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCcaccac                                                 <  2:607259/139‑1 (MQ=255)

                                                                        aaaTCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGc                                               <  2:244679/139‑1 (MQ=255)

                                                                         aaTCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgagag                                                                               >  2:309367/1‑106 (MQ=255)

                                                                         aaTCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgagag                                                                               <  1:309367/106‑1 (MQ=255)

                                                                            ctcACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGt                                           <  2:85300/139‑1 (MQ=255)

                                                                            ctcACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGt                                           <  1:965004/139‑1 (MQ=255)

                                                                                    ggATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAAt                                   <  1:166541/139‑1 (MQ=255)

                                                                                         tGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCa                                                                                                               >  2:1035550/1‑58 (MQ=255)

                                                                                         tGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCa                                                                                                               <  1:1035550/58‑1 (MQ=255)

                                                                                         tGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCtt                              >  2:1334483/1‑139 (MQ=255)

                                                                                           cATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttt                                                                                                                      <  2:1383891/49‑1 (MQ=255)

                                                                                           cATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttt                                                                                                                      >  1:1383891/1‑49 (MQ=255)

                                                                                             tctcTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTtgtg                          >  1:1202992/1‑139 (MQ=255)

                                                                                              ctctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGa                         <  2:1202992/139‑1 (MQ=255)

                                                                                                ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgc                                                                                                                  <  2:601999/48‑1 (MQ=255)

                                                                                                ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgc                                                                                                                  >  1:601999/1‑48 (MQ=255)

                                                                                                ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                                                      >  2:172332/1‑76 (MQ=255)

                                                                                                ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                                                      <  1:172332/76‑1 (MQ=255)

                                                                                                 ttCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCT‑ATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAg                                            >  2:182822/1‑116 (MQ=255)

                                                                                                 ttCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCT‑ATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAg                                            <  1:182822/116‑1 (MQ=255)

                                                                                                     gCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCa                  <  1:1334483/139‑1 (MQ=255)

                                                                                                        aaCCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                >  2:421210/1‑74 (MQ=255)

                                                                                                        aaCCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                <  1:421210/74‑1 (MQ=255)

                                                                                                         aCCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAgttg              <  2:713369/139‑1 (MQ=255)

                                                                                                                     tGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAAt                                   >  2:52124/1‑106 (MQ=255)

                                                                                                                     tGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAAt                                   <  1:52124/106‑1 (MQ=255)

                                                                                                                     tGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATgcgc  >  2:358269/1‑139 (MQ=255)

                                                                                                                     tGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATgcgc  >  2:1432173/1‑139 (MQ=255)

                                                                                                                          cAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATccac                                                    <  1:150172/84‑1 (MQ=255)

                                                                                                                          cAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATccac                                                    >  2:150172/1‑84 (MQ=255)

GATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGC  >  NC_000913/3129450‑3129705

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