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
A12 F28 I1 R1	176	31.5	1082462	98.8%	1069472	138.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,558,955	(T)_5→6	coding (98/1209 nt)	intZ →	CPZ‑55 prophage; putative phage integrase IntZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,558,950	1	.	T	100.0%	105.3 / NA	31	L31L (CTG→CTT)	intZ	CPZ‑55 prophage; putative phage integrase IntZ
Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (15/16); total (15/16)

GATCGGGGTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTG‑TTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAGGCGCGCCACGGAGAG  >  NC_000913/2558819‑2559084

gATCGGGGTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTG‑ttttttgc                                                                                                                                <  1:432726/140‑4 (MQ=255)

gATCGGGGTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTG‑ttttttgc                                                                                                                                <  1:532321/140‑4 (MQ=255)

    ggggTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGt                                                                                                                             >  1:413423/1‑140 (MQ=255)

          aTCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATcc                                                                                                                       >  2:287051/1‑140 (MQ=255)

                tCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCaa                                                                                                                    <  2:494166/137‑1 (MQ=255)

                tCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCaa                                                                                                                    >  1:494166/1‑137 (MQ=255)

                tCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACgg                                                                                                                 >  2:500283/1‑140 (MQ=255)

                             gTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTgg                                                                                                    <  2:413423/140‑1 (MQ=255)

                             gTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTgg                                                                                                    <  1:269092/140‑1 (MQ=255)

                                  cGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGAtt                                                                                               <  2:499293/140‑1 (MQ=255)

                                            cAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTgg                                                                                     <  1:84603/140‑1 (MQ=255)

                                                    cacTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGt                                                                                          <  1:508642/127‑1 (MQ=255)

                                                    cacTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGt                                                                                          >  2:508642/1‑127 (MQ=255)

                                                    cacTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATaa                                                                             >  1:54371/1‑140 (MQ=255)

                                                         acaGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACgag                                                                        >  2:538868/1‑140 (MQ=255)

                                                              aaaGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGttt                                                                   >  2:93694/1‑140 (MQ=255)

                                                                 ggCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTg                                                                <  1:500283/140‑1 (MQ=255)

                                                                   ccATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCa                                                              <  2:461871/140‑1 (MQ=255)

                                                                   ccATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCa                                                              <  2:54371/140‑1 (MQ=255)

                                                                       aGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGcc                                                          >  1:242262/1‑140 (MQ=255)

                                                                            ccgcACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTgg                                                     >  2:20326/1‑140 (MQ=255)

                                                                            ccgcACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTgg                                                     >  1:261028/1‑140 (MQ=255)

                                                                               cacaGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGt                                                  >  1:88592/1‑140 (MQ=255)

                                                                                       cAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGc                                          >  2:465289/1‑140 (MQ=255)

                                                                                           aCAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAAt                                      <  1:360508/140‑1 (MQ=255)

                                                                                            cAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATc                                     <  1:347375/140‑1 (MQ=255)

                                                                                             aaGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATca                                    <  2:88592/140‑1 (MQ=255)

                                                                                               gCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGtt                                                 <  2:161473/125‑1 (MQ=255)

                                                                                               gCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGtt                                                 >  1:161473/1‑125 (MQ=255)

                                                                                                             ccGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACg                    <  1:93694/140‑1 (MQ=255)

                                                                                                                 ttCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAgg                <  2:465760/140‑1 (MQ=255)

                                                                                                                             ggggCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAGGCGCGCCACGgag    <  2:261028/140‑1 (MQ=255)

                                                                                                                               ggCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAGGCGCGCCACGGagag  >  2:509845/1‑140 (MQ=255)

GATCGGGGTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTG‑TTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAGGCGCGCCACGGAGAG  >  NC_000913/2558819‑2559084

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A