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
A6 F73 I1 R1	31	34.8	1203930	99.1%	1193094	139.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,739,564	C→A	intergenic (+37/‑141)	malS → / → avtA	alpha‑amylase/valine‑‑pyruvate aminotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,739,564	0	C	A	100.0%	106.4 / NA	31	intergenic (+37/‑141)	malS/avtA	alpha‑amylase/valine‑‑pyruvate aminotransferase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (11/20); total (11/20)

GGGCAAACAAACGACACTTTTGCTGAAGCAGGGCTACGGCTTTGTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGCCGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTACCTTCCTTGCTACAGAGTTCGACAGATAT  >  NC_000913/3739431‑3739698

gggCAAACAAACGACACTTTTGCTGAAGCAGGGCTACGGCTTTGTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAG‑AACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAAc                                                                                                                                 <  1:266272/140‑1 (MQ=255)

            gACACTTTTGCTGAAGCAGGGCTACGGCTTTGTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAAt                                                                                                                      >  1:262321/1‑140 (MQ=255)

               acTTTTGCTGAAGCAGGGCTACGGCTTTGTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTc                                                                                                                   >  2:497878/1‑140 (MQ=255)

                           gCAGGGCTACGGCTTTGTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAg                                                                                                       <  2:398238/140‑1 (MQ=255)

                               ggCTACGGCTTTGTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGtt                                                                                                   >  1:118934/1‑140 (MQ=255)

                                          tGTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAg                                                                                        <  1:497878/140‑1 (MQ=255)

                                           gTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGc                                                                                       <  2:140650/140‑1 (MQ=255)

                                              cGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCAcc                                                                                    >  1:162350/1‑140 (MQ=255)

                                                 gAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCt                                                                                 <  2:84692/140‑1 (MQ=255)

                                                 gAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCt                                                                                 <  1:289246/140‑1 (MQ=255)

                                                 gAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCt                                                                                 <  2:575830/140‑1 (MQ=255)

                                                               tAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGa                                                                   <  2:158623/140‑1 (MQ=255)

                                                                aaaGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGAc                                                                  <  2:118934/140‑1 (MQ=255)

                                                                      cTGGTCGTCTGGGCAGGGCAACAGTAACTTATCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGAttt                                                            >  1:87538/1‑140 (MQ=255)

                                                                                   cagggcaACAGTAACTTATCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCaaa                                               <  2:87538/140‑1 (MQ=255)

                                                                                      ggcaACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGt                                            <  1:193687/140‑1 (MQ=255)

                                                                                          aCAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACTCCAGCAAATGTAGCg                                        <  2:37990/140‑1 (MQ=255)

                                                                                          aCAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCg                                        <  1:483579/140‑1 (MQ=255)

                                                                                           cAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGt                                       >  1:591875/1‑140 (MQ=255)

                                                                                           cAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGt                                       <  1:234290/140‑1 (MQ=255)

                                                                                                aCTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCACTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTg                                  >  2:117532/1‑140 (MQ=255)

                                                                                                     tCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCg                                        <  2:132765/129‑1 (MQ=255)

                                                                                                     tCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCg                                        >  1:132765/1‑129 (MQ=255)

                                                                                                       cGGCTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTAcctt                           <  2:546244/140‑1 (MQ=255)

                                                                                                          cTTCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTAccttcct                        <  2:530272/140‑1 (MQ=255)

                                                                                                            tCCCGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTACCTTCCTTg                      >  2:283354/1‑140 (MQ=255)

                                                                                                               cGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTACCTTCCTTGCTa                   <  1:482172/140‑1 (MQ=255)

                                                                                                               cGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTACCTTCCTTGCTa                   <  1:273889/140‑1 (MQ=255)

                                                                                                               cGTTCGTCAGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTACCTTCCTCGCTa                   <  2:338522/140‑1 (MQ=255)

                                                                                                                       aGTACCTCGGGAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTACCTTCCTTGCTACAGAGTTc           >  2:535642/1‑140 (MQ=255)

                                                                                                                                ggAAGACGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTACCTTCCTTGCTACAGAGTTCGACAGatat  >  1:300896/1‑140 (MQ=255)

GGGCAAACAAACGACACTTTTGCTGAAGCAGGGCTACGGCTTTGTTCGTGAGCATGGCGACGATAAAGTGCTGGTCGTCTGGGCAGGGCAACAGTAACTTTTCCGGCTTCCCGTTCGTCAGTACCTCGGGAAGCCGCCAACCAGGATAAAATGTCAGCCCTAATCAGCGTTGCAGGATAAAGCACCGCTCACTCTTCAACAGACCGATTTGCACCCCAGCAAATGTAGCGTTATTGTTACCTTCCTTGCTACAGAGTTCGACAGATAT  >  NC_000913/3739431‑3739698

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A