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	4,545,596	T→C	E181G (GAG→GGG)	yjiC ←	YjfZ/YjiC family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,545,596	0	T	C	100.0%	143.6 / NA	39	E181G (GAG→GGG)	yjiC	YjfZ/YjiC family protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (22/17); total (22/17)

GGCTTCTATACCAATTATTGGGTCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCTCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCG  >  NZ_CP009273/4545460‑4545727

ggCTTCTATACCAATTATTGGGTCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCa                                                                                                                                   >  1:192988/1‑139 (MQ=255)

 gCTTCTATACCAATTATTGGGTCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCAt                                                                                                                                  <  2:301255/139‑1 (MQ=255)

                          tACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGc                                                                                                         >  2:86414/1‑139 (MQ=255)

                                aCTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAg                                                                                                   >  1:433624/1‑139 (MQ=255)

                                aCTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAg                                                                                                   >  2:131133/1‑139 (MQ=255)

                                aCTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCCGAGAAGCTGGAAg                                                                                                   >  2:94175/1‑139 (MQ=255)

                                 cTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAgg                                                                                                  >  1:286806/1‑139 (MQ=255)

                                    aaTATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGtt                                                                                               >  2:344354/1‑139 (MQ=255)

                                      tatTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTg                                                                                              >  2:369928/1‑138 (MQ=255)

                                           gCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAata                                                                                         >  1:132076/1‑138 (MQ=255)

                                              ttAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATc                                                                                     >  2:407609/1‑139 (MQ=255)

                                                aaGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAggg                                                                                                 >  2:414899/1‑125 (MQ=255)

                                                aaGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAggg                                                                                                 <  1:414899/125‑1 (MQ=255)

                                                      tGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGa                                                                                                     <  1:116089/115‑1 (MQ=255)

                                                      tGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGa                                                                                                     >  2:116089/1‑115 (MQ=255)

                                                                               tttGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGtt                                                                                               <  1:89172/96‑1 (MQ=255)

                                                                               tttGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGtt                                                                                               >  2:89172/1‑96 (MQ=255)

                                                                                   cTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAAc                                                 <  2:192988/138‑1 (MQ=255)

                                                                                      ccccTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCa                                               <  2:181342/137‑1 (MQ=255)

                                                                                                    aTTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTAttt                               >  2:359384/1‑139 (MQ=255)

                                                                                                          tGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGaa                         >  2:231227/1‑139 (MQ=255)

                                                                                                            aTCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATg                           <  2:433624/135‑1 (MQ=255)

                                                                                                            aTCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGaa                         <  1:94175/137‑1 (MQ=255)

                                                                                                            aTCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGaa                         <  1:131133/137‑1 (MQ=255)

                                                                                                            aTCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGaa                         <  1:359384/137‑1 (MQ=255)

                                                                                                            aTCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGaa                         <  1:369928/137‑1 (MQ=255)

                                                                                                               aaTATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGta                    <  2:177035/139‑1 (MQ=255)

                                                                                                                atatAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGa                                                           <  2:145953/99‑1 (MQ=255)

                                                                                                                atatAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGa                                                           >  1:145953/1‑99 (MQ=255)

                                                                                                                     gATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTc               <  2:404934/138‑1 (MQ=255)

                                                                                                                      atatCAATCCTTGGCTGCCCCTTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATg                           >  1:53745/1‑125 (MQ=255)

                                                                                                                      atatCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCa                                                                    <  2:345542/84‑1 (MQ=255)

                                                                                                                      atatCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCa                                                                    >  1:345542/1‑84 (MQ=255)

                                                                                                                      atatCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATg                           <  2:53745/125‑1 (MQ=255)

                                                                                                                        atCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTc            >  2:239420/1‑138 (MQ=255)

                                                                                                                         tCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCaa          >  2:112729/1‑139 (MQ=255)

                                                                                                                            aTCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAg       <  1:103984/139‑1 (MQ=255)

                                                                                                                                  ggCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCg  >  1:318601/1‑138 (MQ=255)

                                                                                                                                  ggCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCg  >  2:350933/1‑138 (MQ=255)

GGCTTCTATACCAATTATTGGGTCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCTCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCG  >  NZ_CP009273/4545460‑4545727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 17 ≤` `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

GTACCGGGATAGGCTTCTATACCAATTATTGGGTCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCTCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCGAAAGGG  >  NZ_CP009273/4545449‑4545733

GTACCGGGATAGGCTTCTATACCAATTATTGGGTCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCAT                                                                                                                                        >  SRR3722119.195052/1‑151 (MQ=60)

                                GTCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGG                                                                                                        >  SRR3722119.437963/1‑151 (MQ=60)

                                 TCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGG                                                                                                       >  SRR3722119.289763/1‑151 (MQ=60)

                                         gtataagagacagGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAAT                                                                                                <  SRR3722119.117225/137‑1 (MQ=60)

                                           ACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATAT                                                                                              >  SRR3722119.133421/1‑150 (MQ=60)

                                            acagATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATAT                                                                                            <  SRR3722119.419082/147‑1 (MQ=60)

                                                 cgtgggctcggagatgtgtataagagacagATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCC                                                                                          <  SRR3722119.90049/118‑1 (MQ=60)

                                                                                                                TTATCTGATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCctgtctcttatacacatctccgagcccacg                        >  SRR3722119.147453/1‑121 (MQ=60)

                                                                                                                      GATCAATATAGATATCAATCCTTGGCTGCCCCTTGGTCCATCTTTTTGACTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCtgt                  >  SRR3722119.54238/1‑148 (MQ=60)

                                                                                                                      GATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACctgtctcttatacacatctccgagcccacgagactaaggcgaatc                  >  SRR3722119.349051/1‑106 (MQ=60)

                                                                                                                      GATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCC                    <  SRR3722119.373663/149‑1 (MQ=60)

                                                                                                                      GATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCC                    <  SRR3722119.363018/149‑1 (MQ=60)

                                                                                                                      GATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCC                    <  SRR3722119.132460/149‑1 (MQ=60)

                                                                                                                      GATCAATATAGATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCC                    <  SRR3722119.95095/149‑1 (MQ=60)

                                                                                                                                 ATATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCG        >  SRR3722119.417481/1‑150 (MQ=60)

                                                                                                                                  TATCAATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCGA       >  SRR3722119.321857/1‑150 (MQ=60)

                                                                                                                                      AATCCTTGGCTGCCCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCGAAAGGG  <  SRR3722119.105003/151‑1 (MQ=60)

GTACCGGGATAGGCTTCTATACCAATTATTGGGTCATTACCCAACTCAATATTAGCATTAAGTAATGCGGCAAGGGCGAATCCGGAAGAATTTGCTACCCCTGTTACCGTCATTATCTGATCAATATAGATATCAATCCTTGGCTGCTCATTGGTCCATCTTTTTGCCTGAGAAGCTGGAAGGGTTGAAATATATCCTATCGTGGTTCCGGCATAACCAGGAACATTGCAACCAGGGCCTAATGTTATTTCATGAACTGTATAGTCCTCAACAGGATCGAAAGGG  >  NZ_CP009273/4545449‑4545733

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`