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
A3 F50 I1 R1	300	54.7	1718999	98.4%	1691495	149.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,883,255	C→T	D159N (GAT→AAT)	dnaA ←	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,883,255	0	C	T	100.0%	172.7 / NA	46	D159N (GAT→AAT)	dnaA	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (20/26); total (20/26)

CGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATCCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGTAGAAGGC  >  NC_000913/3883120‑3883400

cGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGa                                                                                                                                      <  1:34247/149‑1 (MQ=255)

    gTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAgccgcc                                                                                                                                >  1:362360/1‑151 (MQ=255)

           taAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCcgcgcgcg                                                                                                                         >  1:268427/1‑151 (MQ=255)

               ccACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCa                                                                                                                      <  2:402264/150‑1 (MQ=255)

                     tGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGtt                                                                                                               >  2:33110/1‑151 (MQ=255)

                     tGGAATCCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCCCCTGGCGAGCCGCCGCGCGCGCCAGTTgg                                                                                                                 <  2:359698/149‑1 (MQ=255)

                        cATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGa                                                                                                            <  2:131485/151‑1 (MQ=255)

                          ttCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGAtt                                                                                                          >  2:656778/1‑151 (MQ=255)

                              gCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTAcc                                                                                                      <  2:788920/151‑1 (MQ=255)

                                  gcgcgcCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCa                                                                                                  <  1:133180/151‑1 (MQ=255)

                                     cgcCATAATGCCGTTACCCACCGCAGGCAGCAGGTGAGTTTTACCCGGACCCGGGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCaa                                                                                                 <  1:657078/149‑1 (MQ=255)

                                        cATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAg                                                                                            <  1:193892/151‑1 (MQ=255)

                                         aTAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGt                                                                                           <  1:707558/151‑1 (MQ=255)

                                          tAATGCCGTTACCCCCCGCATGCAGCAGGTGGGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAg                                                                                            <  1:592065/149‑1 (MQ=255)

                                           aaTGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGtt                                                                                          <  1:344854/150‑1 (MQ=255)

                                           aaTGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGtt                                                                                          >  2:472000/1‑150 (MQ=255)

                                                             aTGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACg                                                                       <  2:71599/151‑1 (MQ=255)

                                                               gcagcaGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGtt                                                                     <  1:321998/151‑1 (MQ=255)

                                                                  gcagGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGttt                                                                    <  2:566249/149‑1 (MQ=255)

                                                                  gcagGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTAc                                                                  <  2:654385/151‑1 (MQ=255)

                                                                   cagGTGAGTTTTCCCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACg                                                                 <  1:444065/151‑1 (MQ=255)

                                                                           ttttACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAAc                                                          <  1:688361/150‑1 (MQ=255)

                                                                              tACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGAt                                                       >  2:103793/1‑150 (MQ=255)

                                                                                 ccAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGt                                                   >  2:109086/1‑151 (MQ=255)

                                                                                      cccGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCg                                                 <  2:185302/148‑1 (MQ=255)

                                                                                      cccGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGt                                               <  1:73428/150‑1 (MQ=255)

                                                                                         gTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTg                                           <  2:677736/151‑1 (MQ=255)

                                                                                             cgccATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACg                                                                 <  1:248335/125‑1 (MQ=255)

                                                                                             cgccATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACg                                                                 >  2:248360/1‑125 (MQ=255)

                                                                                               ccATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggg                                      <  1:443088/150‑1 (MQ=255)

                                                                                               ccATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggg                                      <  1:548597/150‑1 (MQ=255)

                                                                                                   aaaGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggggccgg                                 >  1:101008/1‑151 (MQ=255)

                                                                                                     aGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggggccggg                                >  1:473581/1‑150 (MQ=255)

                                                                                                     aGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggggccggg                                >  2:715785/1‑150 (MQ=255)

                                                                                                         acaacGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGtt                           >  1:329003/1‑151 (MQ=255)

                                                                                                           aacGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTAt                         >  2:626687/1‑151 (MQ=255)

                                                                                                           aacGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTAt                         >  1:422305/1‑151 (MQ=255)

                                                                                                             cGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATcc                       >  1:303889/1‑151 (MQ=255)

                                                                                                              gggTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATccc                      >  1:176761/1‑151 (MQ=255)

                                                                                                                   ataGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCt                 >  1:346135/1‑151 (MQ=255)

                                                                                                                     aGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGa               <  1:477651/151‑1 (MQ=255)

                                                                                                                         aCCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAgcgc           >  1:626145/1‑151 (MQ=255)

                                                                                                                             ccAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGTAg       <  2:366114/151‑1 (MQ=255)

                                                                                                                              cAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGt         >  2:313481/1‑148 (MQ=255)

                                                                                                                                 ggTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGTAGAAgg   >  1:86531/1‑151 (MQ=255)

                                                                                                                                   ttATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGTAGAAGgc  <  2:847166/150‑1 (MQ=255)

CGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATCCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGTAGAAGGC  >  NC_000913/3883120‑3883400

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A