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 F1 I1 R1	748	32.0	1685426	92.6%	1560704	103.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,053,940	A→G	T100A (ACC→GCC)	shiA →	shikimate transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,053,940	0	A	G	100.0%	70.8 / NA	21	T100A (ACC→GCC)	shiA	shikimate transporter
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/12); total (9/12)

AAGTAAGCCCGGCGATGGGAACGCTCGCCGCATTTGCTACCTTTGGCGTCGGATTTCTTTTCCGTCCGCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGACCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTGCCATTCAGGGATTTGCAGTCGGCGGCGAAT  >  NC_000913/2053809‑2054069

aaGTAAGCCCGGCGATGGGAACGCTCGCCGCATTTGCTACCTTTGGCGTCGGATTTCTTTTCCGTCCGCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTg                                                                                                                            >  1:764873/1‑139 (MQ=255)

       cccGGCGATGGGAACGCTCGCCGCATTTGCTACCTTTGGCGTCGGATTTCTTTTCCGTCCGCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGatgatg                                                                                                                     <  2:764873/139‑1 (MQ=255)

                   aaCGCTCGCCGCATTTGCTACCTTTGGCGTCGGATTTCTTTTCCGTCCGCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACa                                                                                                         >  1:312011/1‑139 (MQ=255)

                                    cTACCTTTGGCGTCGGATTTCTTTTCCGTCCGCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTAttct                                                                                        >  1:57104/1‑139 (MQ=255)

                                                  ggATTTCTTTTCCGTCCGCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGa                                                                          <  2:732172/139‑1 (MQ=255)

                                                          tttCCGTCCGCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTggg                                                                  <  2:312011/139‑1 (MQ=255)

                                                                tccgCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGgat                                                                                                                         <  1:398463/78‑1 (MQ=255)

                                                                tccgCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGgat                                                                                                                         >  2:398463/1‑78 (MQ=255)

                                                                  cgCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGc                                                          <  1:364119/139‑1 (MQ=255)

                                                                                      ggTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGAt                                                                                                 <  2:81268/80‑1 (MQ=255)

                                                                                      ggTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGAt                                                                                                 >  1:81268/1‑80 (MQ=255)

                                                                                            tttGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTg                                <  2:439622/139‑1 (MQ=255)

                                                                                                               gTAAGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTGCCATTCAGGGATTTGCAGt             <  1:136521/139‑1 (MQ=255)

                                                                                                                  aGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTg                                <  2:4706/117‑1 (MQ=255)

                                                                                                                  aGCGCATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTg                                >  1:4706/1‑117 (MQ=255)

                                                                                                                    cgcATGTTAATGCTGGTCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTGCCATTCAGGGATTTGCAGTcggcg        <  2:109134/139‑1 (MQ=255)

                                                                                                                    cgcATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTGCCATTCAGGGATTTGCAGTcggcg        <  2:196740/139‑1 (MQ=255)

                                                                                                                      cATGTTAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTGCCATTCAGGGATTTGCAGTCggcggc      >  1:737727/1‑139 (MQ=255)

                                                                                                                          ttAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTg                                >  1:646280/1‑109 (MQ=255)

                                                                                                                          ttAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTg                                <  2:646280/109‑1 (MQ=255)

                                                                                                                          ttAATGCTGGCCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTGCCATTCAGGGATTTGCAGTCGGCGGCGAAt  >  1:354303/1‑139 (MQ=255)

AAGTAAGCCCGGCGATGGGAACGCTCGCCGCATTTGCTACCTTTGGCGTCGGATTTCTTTTCCGTCCGCTCGGCGGTGTCATTTTCGGTCACTTTGGCGACCGACTGGGACGTAAGCGCATGTTAATGCTGACCGTCTGGATGATGGGCATCGCGACAGCCTTGATTGGTATTCTTCCTTCATTCTCGACCATTGGGTGGTGGGCACCTATTTTGCTGGTGACACTGCGTGCCATTCAGGGATTTGCAGTCGGCGGCGAAT  >  NC_000913/2053809‑2054069

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A