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
A2 F50 I1 R1	170	39.5	1266514	99.2%	1256381	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,228,525	G→A	pseudogene (85/1287 nt)	mdtQ ←	pseudogene; putative channel/filament proteins

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,228,525	0	G	A	100.0%	137.3 / NA	35	pseudogene (85/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (17/18); total (17/18)

AAACGGCCCCATTAAGCCTTCTGCCGACATTTTTTGCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGGTGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTG  >  NC_000913/2228382‑2228671

aaaCGGCCCCATTAAGCCTTCTGCCGACATTTTTTGCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTc                                                                                                                                             >  1:177323/1‑151 (MQ=255)

       cccATTAAGCCTTCTGCCGACATTTTTTGCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTg                                                                                                                                      <  1:561984/151‑1 (MQ=255)

                 cTTCTGCCGACATTTTTTGCCGCCCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGttaat                                                                                                                            >  2:617445/1‑151 (MQ=255)

                      gCCGACATTTTTTGCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAgg                                                                                                                       <  2:564266/151‑1 (MQ=255)

                               ttttGCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGtt                                                                                                              >  2:414549/1‑151 (MQ=255)

                                 ttGCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTg                                                                                                             <  1:563431/150‑1 (MQ=255)

                                   gCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGAtt                                                                                                          <  2:82864/151‑1 (MQ=255)

                                   gCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGAt                                                                                                           <  2:422247/150‑1 (MQ=255)

                                    ccGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGAtt                                                                                                          >  2:166201/1‑150 (MQ=255)

                                           atatCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGAt                                                                                                  >  1:573759/1‑151 (MQ=255)

                                             atCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATa                                                                                                 <  2:164672/150‑1 (MQ=255)

                                              tCCGCCGAAAAGTCGATCTGCGGACCATCCTGGGTGGCAACTGCTTTCGCCTGGGCTTCACATAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTCGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACt                                                                                               >  2:490752/1‑151 (MQ=255)

                                                 gccgAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCa                                                                                            <  2:171151/151‑1 (MQ=255)

                                                          tCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCAtt                                                                                   >  2:137541/1‑151 (MQ=255)

                                                                tGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGt                                                                             >  2:602554/1‑151 (MQ=255)

                                                                 gCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTgg                                                                                 <  2:301429/146‑1 (MQ=255)

                                                                 gCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGc                                                                                <  1:452984/147‑1 (MQ=255)

                                                                 gCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCt                                                                               <  2:239167/148‑1 (MQ=255)

                                                                    gACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTgg                                                                         <  1:549752/151‑1 (MQ=255)

                                                                       cATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGcc                                                                       >  1:32749/1‑150 (MQ=255)

                                                                        aTCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCa                                                                      >  2:548098/1‑150 (MQ=255)

                                                                             gAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCAtt                                                                >  2:494005/1‑151 (MQ=255)

                                                                                     aCTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAgcgc                                                        <  2:22314/151‑1 (MQ=255)

                                                                                            tCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGt                                                 >  1:199732/1‑151 (MQ=255)

                                                                                             cGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTa                                                <  2:493106/151‑1 (MQ=255)

                                                                                                                  aaTGCGCTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCCGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGc                             >  2:57404/1‑149 (MQ=255)

                                                                                                                     gcgcTGTTCAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCgg                        <  1:137785/151‑1 (MQ=255)

                                                                                                                             cAGCCACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGc                <  2:123600/151‑1 (MQ=255)

                                                                                                                                 cACCTGCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGc            <  1:477551/151‑1 (MQ=255)

                                                                                                                                      gCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAAc       <  2:462991/151‑1 (MQ=255)

                                                                                                                                      gCATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAAc       >  1:598869/1‑151 (MQ=255)

                                                                                                                                       cATATCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACg      >  1:218773/1‑151 (MQ=255)

                                                                                                                                        atatCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGc     >  2:542532/1‑151 (MQ=255)

                                                                                                                                          atCCGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCt   >  1:173278/1‑151 (MQ=255)

                                                                                                                                            ccGATGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTg  <  2:490966/150‑1 (MQ=255)

AAACGGCCCCATTAAGCCTTCTGCCGACATTTTTTGCCGCTCCATATCCGCCGAAAAGTCGATCTGCGGACCATCCTGAGTGGCAACTGCCTTCGCCTGGGCTTCAGCTAGCTGAATGCGCTGTTCAGCCACCTGCATATCCGGTGCGTTCTGTAGTGCATTGTTAATTAAGGAAGTGAGTTGATTATCGTGATACTCCAGCCACCATTGGCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTG  >  NC_000913/2228382‑2228671

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A