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
A1 F4 I96 R1	227	23.3	882352	98.0%	864704	126.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	870,468	A→G	Q678Q (CAA→CAG)	pdeI →	EAL domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	870,468	0	A	G	100.0%	102.4 / NA	28	Q678Q (CAA→CAG)	pdeI	EAL domain‑containing protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (18/10); total (18/10)

AGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTG  >  NZ_CP009273/870341‑870603

aGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGat                                                                                                                              <  2:88280/139‑1 (MQ=255)

     tttACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGa                                                                                                                         >  2:273156/1‑139 (MQ=255)

               tcatGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACtt                                                                                                               >  2:412691/1‑139 (MQ=255)

               tcatGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACtt                                                                                                               >  2:269073/1‑139 (MQ=255)

               tcatGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACtt                                                                                                               >  1:95788/1‑139 (MQ=255)

                      agaaaATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCAcc                                                                                                        >  1:139700/1‑139 (MQ=255)

                               ccTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCa                                                                                               <  1:244486/139‑1 (MQ=255)

                               ccTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCa                                                                                               <  2:99292/139‑1 (MQ=255)

                                                  tgtgTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTa                                                                              <  1:317961/137‑1 (MQ=255)

                                                        gagaTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAAtt                                                                       >  1:218768/1‑138 (MQ=255)

                                                              aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc                                                                   >  2:390953/1‑136 (MQ=255)

                                                              aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc                                                                   >  2:25032/1‑136 (MQ=255)

                                                              aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc                                                                   >  2:432405/1‑136 (MQ=255)

                                                              aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc                                                                   >  1:44111/1‑136 (MQ=255)

                                                               cTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa                                                               <  1:269073/139‑1 (MQ=255)

                                                                        tGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATa                                                        >  2:9170/1‑137 (MQ=255)

                                                                              aGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGa                                                >  1:341546/1‑139 (MQ=255)

                                                                              aGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGa                                                >  2:383047/1‑139 (MQ=255)

                                                                                                  tATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGat                             <  1:273156/138‑1 (MQ=255)

                                                                                                               aacaacTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGc               >  1:362250/1‑139 (MQ=255)

                                                                                                                    cTGCGTAAGCAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGCAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGa           >  1:415556/1‑138 (MQ=255)

                                                                                                                    cTGCGTAAACAGGGGGTACGTATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa                                                               <  1:143314/86‑1 (MQ=255)

                                                                                                                    cTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa                                                               <  2:36099/86‑1 (MQ=255)

                                                                                                                    cTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa                                                               >  1:36099/1‑86 (MQ=255)

                                                                                                                    cTGCGTAAACAGGGGGTAAGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa                                                               >  2:143314/1‑86 (MQ=255)

                                                                                                                       cGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGaaaaa       >  2:176112/1‑139 (MQ=255)

                                                                                                                            aCAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATtgtg  <  1:9170/139‑1 (MQ=255)

                                                                                                                            aCAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATtgtg  <  2:95788/139‑1 (MQ=255)

AGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTG  >  NZ_CP009273/870341‑870603

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTT  >  NZ_CP009273/870345‑870614

TTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTT                                                                                                                         >  SRR3722119.96728/1‑151 (MQ=60)

       ACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCG                                                                                                                  >  SRR3722119.141150/1‑151 (MQ=60)

                          GCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACG                                                                                               <  SRR3722119.247032/151‑1 (MQ=60)

                                         GCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTA                                                                                 >  SRR3722119.221108/1‑150 (MQ=60)

                                             CTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATC                                                                              <  SRR3722119.321211/149‑1 (MQ=60)

                                               GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCC                                                                             >  SRR3722119.44501/1‑148 (MQ=60)

                                                          ACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG                                                               <  SRR3722119.271856/151‑1 (MQ=60)

                                                           tccccttagtctcgtgggctcggagatgtgtataagagacagATATTGAACAACTGCGTAAACAGGGGGTACGTATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG                                                               <  SRR3722119.144797/108‑1 (MQ=60)

                                                               AACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGAC                                                          >  SRR3722119.345027/1‑151 (MQ=60)

                                                                                             TTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTAC                             <  SRR3722119.275991/150‑1 (MQ=60)

                                                                                                TCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCG                         >  SRR3722119.365905/1‑151 (MQ=60)

                                                                                                     ATATTGAACAACTGCGTAAGCAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGCAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCACTTCACCGGCGATATTTTCGGTACTGCGGGAA                     >  SRR3722119.419742/1‑150 (MQ=60)

                                                                                                     ATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGctgtctcttatacacatctccgagcccacgagactaaggcga                     >  SRR3722119.36417/1‑108 (MQ=60)

                                                                                                                  GCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATT       >  SRR3722119.435361/1‑151 (MQ=60)

                                                                                                                       AACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTT  >  SRR3722119.399253/1‑151 (MQ=60)

                                                                                                                       AACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTT  <  SRR3722119.9241/151‑1 (MQ=60)

TTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTT  >  NZ_CP009273/870345‑870614

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`