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
A1 F28 I1 R1	163	52.9	1786516	99.3%	1774010	139.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,334,268	G→A	pseudogene (135/4605 nt)	yfaS ←	putative macroglobulin family protein, N‑terminal fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,334,268	0	G	A	100.0%	124.4 / NA	36	pseudogene (135/4605 nt)	yfaS	putative macroglobulin family protein, N‑terminal fragment
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (14/22); total (14/22)

CTCTTCCATCTGATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATC  >  NC_000913/2334142‑2334403

ctctTCCATCTGATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCg                                                                                                                            <  2:198078/140‑1 (MQ=255)

 tctTCCATCTGATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGa                                                                                                                           <  2:605966/140‑1 (MQ=255)

 tctTCCATCTGATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTAGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGa                                                                                                                           <  1:775637/140‑1 (MQ=255)

        tCTGATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAAtcatca                                                                                                                    >  2:781774/1‑140 (MQ=255)

           gATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCa                                                                                                                 >  1:42136/1‑140 (MQ=255)

           gATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCa                                                                                                                 <  2:318861/140‑1 (MQ=255)

           gATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCa                                                                                                                 <  2:198060/140‑1 (MQ=255)

             tAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCAtt                                                                                                               >  1:523631/1‑140 (MQ=255)

                         tCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGt                                                                                                   <  1:781774/140‑1 (MQ=255)

                            cGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTcc                                                                                                >  2:99080/1‑140 (MQ=255)

                               cccGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCcac                                                                                             >  2:120327/1‑140 (MQ=255)

                                ccGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCcaca                                                                                            <  1:82709/140‑1 (MQ=255)

                                 cGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCcaca                                                                                            <  1:294573/139‑1 (MQ=255)

                                 cGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCcaca                                                                                            >  2:294573/1‑139 (MQ=255)

                                  ggCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAag                                                                                          >  2:58135/1‑140 (MQ=255)

                                   gcgcTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAACCTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAaga                                                                                         <  1:148792/140‑1 (MQ=255)

                                         ccAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAgg                                                                                   <  1:890691/140‑1 (MQ=255)

                                               gCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAg                                                                             <  2:190364/140‑1 (MQ=255)

                                               gCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAg                                                                             <  1:656533/140‑1 (MQ=255)

                                                 aCTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCa                                                                           <  2:355887/140‑1 (MQ=255)

                                                 aCTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCa                                                                           <  2:523631/140‑1 (MQ=255)

                                                  cTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCa                                                                           >  1:7506/1‑139 (MQ=255)

                                                  cTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCa                                                                           <  2:7506/139‑1 (MQ=255)

                                                   tttCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACg                                                                         <  2:274022/140‑1 (MQ=255)

                                                        ccTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACgctgct                                                                    >  1:390346/1‑140 (MQ=255)

                                                            ttCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATcg                                                                >  2:125755/1‑140 (MQ=255)

                                                                  gctgctAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAg                                                          >  1:738709/1‑140 (MQ=255)

                                                                        aaaaCTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAAtt                                                    >  2:377613/1‑140 (MQ=255)

                                                                             tgctgTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAAc                                               >  1:697895/1‑140 (MQ=255)

                                                                                    agcaagcaAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAAt                                        <  1:99080/140‑1 (MQ=255)

                                                                                               aGAATGTTCCCCCGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAAt                             <  2:738709/140‑1 (MQ=255)

                                                                                                       cccccGGCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTg                     >  1:767347/1‑140 (MQ=255)

                                                                                                            ggCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATc                <  2:459117/140‑1 (MQ=255)

                                                                                                            ggCAGGCGGCGCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATc                <  1:377613/140‑1 (MQ=255)

                                                                                                                  cggcgCATAGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTggg          <  2:767347/140‑1 (MQ=255)

                                                                                                                          aGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATc  <  2:126338/140‑1 (MQ=255)

                                                                                                                          aGTTACTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATc  <  2:390346/140‑1 (MQ=255)

CTCTTCCATCTGATAGCGCCGATAATCACGCCCCGGCGCTTCCAGTCGCACTTTCGCCTCTTCACTGCTGCTAAAACTGCTGTCAGCAAGCAAAAAGAATGTTCCCCCGGCAGGCGGCGCATAGTTGCTGGAAGGAAGCGAATCATCAGCATTAGCAAGCCCTGTTCCCACAAGAGACAGGGACAAGCACGCTGCTATCGCGCCAGAAAATTTAAACGATAAATGCCAATGAAATTGGGATTGGAATCGTTGGGTATCCATC  >  NC_000913/2334142‑2334403

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A