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
A14 F1 I2 R1	774	49.2	2112398	96.9%	2046913	118.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,889,432	G→A	N105N (AAC→AAT)	fadD ←	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,889,432	0	G	A	100.0%	160.8 / NA	50	N105N (AAC→AAT)	fadD	acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (29/21); total (29/21)

GTCAGAATTACGTGCTGAACGGCGGTTTTATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGGTTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGCCCCAACCCTTGTTGCAAATAAG  >  NC_000913/1889298‑1889559

gTCAGAATTACGTGCTGAACGGCGGTTTTATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACATTCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTaa                                                                                                                             >  1:636197/1‑139 (MQ=255)

  cAGAATTACGTGCTGAACGGCGGTTTTATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACg                                                                                                                           >  2:838832/1‑139 (MQ=255)

          cGTGCTGAACGGCGGTTTTATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTacgac                                                                                                                   >  1:923747/1‑139 (MQ=255)

          cGTGCTGAACGGCGGTTTTATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCCCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTacgac                                                                                                                   >  1:428270/1‑139 (MQ=255)

            tGCTGAACGGCGGTTTTATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGAAGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTAcgacga                                                                                                                 >  2:27999/1‑139 (MQ=255)

                      cggTTTTATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGc                                                                                                       >  2:573794/1‑139 (MQ=255)

                           ttATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCa                                                                                                  <  2:394314/139‑1 (MQ=255)

                                aaCCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATg                                                                                             >  2:105456/1‑139 (MQ=255)

                                        tttCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAg                                                                                     <  2:636197/139‑1 (MQ=255)

                                        tttCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAg                                                                                     <  2:621541/139‑1 (MQ=255)

                                                  gtgAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGa                                                                           <  2:536167/139‑1 (MQ=255)

                                                   tgAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCa                                                                                                  >  2:282884/1‑115 (MQ=255)

                                                   tgAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCa                                                                                                  <  1:282884/115‑1 (MQ=255)

                                                   tgAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGat                                                                          <  1:573794/139‑1 (MQ=255)

                                                    gAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGata                                                                         <  2:292097/139‑1 (MQ=255)

                                                         aaGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCa                                                                    <  1:838832/139‑1 (MQ=255)

                                                         aaGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTGAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATTATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCa                                                                    <  1:705410/139‑1 (MQ=255)

                                                           gTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAAt                                                                  >  2:844396/1‑139 (MQ=255)

                                                               gagacGATAACGATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTAACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAAt                                                              >  2:611829/4‑139 (MQ=255)

                                                               gACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAAt                                                              >  2:709044/1‑139 (MQ=255)

                                                                    gATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAg                                                                                     <  1:723035/111‑1 (MQ=255)

                                                                    gATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAg                                                                                     >  2:723035/1‑111 (MQ=255)

                                                                    gATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGc                                                         >  2:676749/1‑139 (MQ=255)

                                                                              gCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCaa                                                                   <  1:726092/119‑1 (MQ=255)

                                                                              gCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCaa                                                                   >  2:726092/1‑119 (MQ=255)

                                                                              gCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATcaacg                                               >  1:359935/1‑139 (MQ=255)

                                                                               ccGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATcaacgc                                              >  2:365159/1‑139 (MQ=255)

                                                                                   tGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATcaacgcaacg                                          >  2:296278/1‑139 (MQ=255)

                                                                                    gcgcCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCaacgcaacgc                                         >  2:787482/1‑139 (MQ=255)

                                                                                       ccgcTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGAt                                      <  1:97626/139‑1 (MQ=255)

                                                                                       ccgcTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGAt                                      <  1:145550/139‑1 (MQ=255)

                                                                                          cTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGc                                   >  2:15495/1‑139 (MQ=255)

                                                                                            aTCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCt                                 <  1:709044/139‑1 (MQ=255)

                                                                                                  aaGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTttcttc                           <  1:296278/139‑1 (MQ=255)

                                                                                                  aaGCTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTttcttc                           >  2:364953/1‑139 (MQ=255)

                                                                                                     cTGATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGc                        <  2:198900/139‑1 (MQ=255)

                                                                                                       gATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCaa                                                                   >  2:333002/1‑94 (MQ=255)

                                                                                                       gATGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCaa                                                                   <  1:333002/94‑1 (MQ=255)

                                                                                                        aTGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGcccc                     >  1:631572/1‑139 (MQ=255)

                                                                                                        aTGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGcccc                     >  1:34122/1‑139 (MQ=255)

                                                                                                         tGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCa                                                                                                      >  1:999338/1‑57 (MQ=255)

                                                                                                         tGCTCAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCa                                                                                                      <  2:999338/57‑1 (MQ=255)

                                                                                                             cAAGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGCCCCAAccc                <  1:364953/139‑1 (MQ=255)

                                                                                                              aaGCTCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGCCCCAACCCt               >  2:301320/1‑139 (MQ=255)

                                                                                                                  tCACGCGGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGCCCCAACCCttgtt           >  1:397362/1‑139 (MQ=255)

                                                                                                                       cgGGGTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGCCCCAACCCTTGTTGCaaa      <  2:359935/139‑1 (MQ=255)

                                                                                                                          ggTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTg                                                                      <  1:138347/72‑1 (MQ=255)

                                                                                                                          ggTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTg                                                                      >  2:138347/1‑72 (MQ=255)

                                                                                                                           gTATACAACGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGCCCCAACCCTTGTTGCAAATAAg  >  1:813378/1‑139 (MQ=255)

                                                                                                                                   cGGATTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCa                                                                    >  2:200845/1‑65 (MQ=255)

GTCAGAATTACGTGCTGAACGGCGGTTTTATCAACCACTTTTTCCAGTGTGTGAGCAAAGTTAGACACGATAACAATCGCCGATGCGCCGCTATCGTTAAGCTGATGCTCAAGCTCACGCGGGGTATACAACGGGTTAACGTTTACGACGATCATCCCGGCACGCAAAATGCCAAACAGCGCCACCGGATATTGCAATAAATTAGGCATCATCAACGCAACGCGATCGCCTTTCTTCAGCCCCAACCCTTGTTGCAAATAAG  >  NC_000913/1889298‑1889559

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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