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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,502,011	A→G	intergenic (+422/+92)	yjgZ → / ← insG	uncharacterized protein/IS4 transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,502,011	0	A	G	100.0%	160.4 / NA	45	intergenic (+422/+92)	yjgZ/insG	uncharacterized protein/IS4 transposase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (21/24); total (21/24)

CCTTACCAATTAAGGGACATAGCCAGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGACAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAACTGACTGGCTCTTTTTCGGGGCTGTGGGGTA  >  NC_000913/4501877‑4502141

ccTTACCAATTAAGGGACATAGCCAGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTGGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGAGTTGACGGTCAGTCTTGGGTGCaaa                                                                                                                                <  2:886754/139‑1 (MQ=255)

      cAATTAAGGGACATAGCCAGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCt                                                                                                                          <  2:897622/139‑1 (MQ=255)

              ggACATAGCCAGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATtc                                                                                                                  >  2:7489/1‑139 (MQ=255)

                  aTAGCCAGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGt                                                                                                              >  1:289840/1‑139 (MQ=255)

                    aGCCAGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTg                                                                                                            >  1:703922/1‑139 (MQ=255)

                        aGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCaaaaaa                                                                                                                             <  2:191144/118‑1 (MQ=255)

                        aGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCaaaaaa                                                                                                                             >  1:191144/1‑118 (MQ=255)

                                     gCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCt                                                                                                                          <  1:582303/108‑1 (MQ=255)

                                     gCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCt                                                                                                                          >  2:582303/1‑108 (MQ=255)

                                                   tCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCt                                                                                <  1:406459/136‑1 (MQ=255)

                                                   tCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCt                                                                                >  2:406459/1‑136 (MQ=255)

                                                             ttAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCt                                                                                                                          <  2:722007/84‑1 (MQ=255)

                                                             ttAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCt                                                                                                                          >  1:722007/1‑84 (MQ=255)

                                                             ttAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAgg                                                                   >  1:185101/1‑139 (MQ=255)

                                                             ttAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAgg                                                                   >  2:46215/1‑139 (MQ=255)

                                                             ttAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAgg                                                                   <  1:7489/139‑1 (MQ=255)

                                                             ttAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAgg                                                                   >  2:854206/1‑139 (MQ=255)

                                                                  tCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCt                                                              <  1:764043/139‑1 (MQ=255)

                                                                  tCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCt                                                              <  1:46215/139‑1 (MQ=255)

                                                                    cGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGa                                                                                                   <  1:578995/100‑1 (MQ=255)

                                                                    cGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGa                                                                                                   >  2:578995/1‑100 (MQ=255)

                                                                    cGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAAtt                                                                                              <  2:161631/105‑1 (MQ=255)

                                                                    cGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAAtt                                                                                              >  1:161631/1‑105 (MQ=255)

                                                                     gCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTgg                                                           <  1:854206/139‑1 (MQ=255)

                                                                     gCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTgg                                                           <  2:271600/139‑1 (MQ=255)

                                                                           cTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGt                                                     <  2:185101/139‑1 (MQ=255)

                                                                                           gTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAAc                                                                                                       >  1:909837/1‑73 (MQ=255)

                                                                                           gTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAAc                                                                                                       <  2:909837/73‑1 (MQ=255)

                                                                                           gTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGc                                                                                 >  1:800659/1‑95 (MQ=255)

                                                                                           gTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGc                                                                                 <  2:800659/95‑1 (MQ=255)

                                                                                           gTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTaa                                     >  1:370888/1‑139 (MQ=255)

                                                                                               aaCAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCaa                                 >  2:396646/1‑139 (MQ=255)

                                                                                                aCAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAac                                >  2:264359/1‑139 (MQ=255)

                                                                                                    tgaaaGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGGCAGTCAGTTAAGCAactgac                            <  2:546269/137‑1 (MQ=255)

                                                                                                    tCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGaaa                                                                            <  2:447082/91‑1 (MQ=255)

                                                                                                    tCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGaaa                                                                            >  1:447082/1‑91 (MQ=255)

                                                                                                    tCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAactgac                            <  1:654586/139‑1 (MQ=255)

                                                                                                    tCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAactgac                            <  1:396646/139‑1 (MQ=255)

                                                                                                     cAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAactgact                           <  2:289840/139‑1 (MQ=255)

                                                                                                            tgtgGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCcagtc                                           >  1:653804/1‑116 (MQ=255)

                                                                                                            tgtgGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCcagtc                                           <  2:653804/116‑1 (MQ=255)

                                                                                                              tgGCGTTGACGGTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAACTGACTGGCTCtttt                  >  2:772857/1‑139 (MQ=255)

                                                                                                                        ggTCAGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAACTGACTGGCTCTTTTTCGGGGCtgt        <  1:772857/139‑1 (MQ=255)

                                                                                                                            aGTCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAACTGACTGGCTCTTTTTCGGGGCTGTgggg    <  1:418505/139‑1 (MQ=255)

                                                                                                                              tCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGGTGCTGAAACGAAATAGGCATCTTGGTGCTGAAATGCCAGTCAGTTAAGCAACTGACTGGCTCTTTTTGGGGGCTGTGGGGTa  <  2:785096/139‑1 (MQ=255)

                                                                                                                              tCTTGGGGGCAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAACTGACTGGCTCTTTTTCGGGGCTGTGGGGTa  >  2:722743/1‑139 (MQ=255)

CCTTACCAATTAAGGGACATAGCCAGATACGCAACTGGCTGATGCAAGCAGTCTAATGTCTTTAGATCCGCTGGCCTGCGGGCATGACAATGTCAAACAGTCAAAGATTGTGGCGTTGACGGTCAGTCTTGGGGACAAAAAAGCTCAGTATTCTCGTTGGCAACCAGATAATTTAACAGTTGATGCTGAAACGAAATAGGCATCTTGGTTCTGTAATGCCAGTCAGTTAAGCAACTGACTGGCTCTTTTTCGGGGCTGTGGGGTA  >  NC_000913/4501877‑4502141

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A