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
A11 F58 I0 R3	223	82.2	2922920	95.2%	2782619	126.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP006881	2,963,937	G→A	11.5%	intergenic (‑124/+156)	U712_15285 ← / ← U712_15290	Manganese‑binding lipoprotein mntA/o‑succinylbenzoate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,963,937	0	G	A	11.5%	125.3 / 7.1	46	intergenic (‑124/+156)	U712_15285/U712_15290	Manganese‑binding lipoprotein mntA/o‑succinylbenzoate synthase
Reads supporting (aligned to +/- strand): ref base G (31/8); new base A (3/2); total (34/12)
Fisher's exact test for biased strand distribution p-value = 3.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.64e-01

AGCCCTTGTCTCATATTTCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCATTT  >  CP006881/2963800‑2964066

aGCCCTTGTCTCATATTTCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATg                                                                                                                                    <  2:125378/138‑1 (MQ=255)

  cccTTGTCTCATATTTCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCa                                                                                                                                  >  8:164089/1‑138 (MQ=255)

      tGTCTCATATTTCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAAtt                                                                                                                             >  2:178035/1‑139 (MQ=255)

            atatTTCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATcgcg                                                                                                                       >  5:345999/1‑139 (MQ=255)

             tatTTCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATACAAAATTATCGCGt                                                                                                                      >  4:257469/1‑139 (MQ=255)

                  ctcctcctcTTTGCCATCCATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCACGTTTgg                                                                                                                  <  8:359162/138‑1 (MQ=255)

                  ctcctcctcTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGc                                                                                                                 >  1:80767/1‑139 (MQ=255)

                  ctcctcctcTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGc                                                                                                                 >  2:263821/1‑139 (MQ=255)

                  ctcctcctcTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCCCATGCAAAATTATCGAGTTTGGc                                                                                                                 >  7:358165/1‑139 (MQ=255)

                     ctcctcTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATACAAAATTATCGCGTTTGGc                                                                                                                 <  3:257469/136‑1 (MQ=255)

                     ctcctcTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCCCATGCAAAATTATCGCGTTTGGCCAt                                                                                                              <  8:358165/139‑1 (MQ=255)

                        ctctTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATACAAAATTATCGCGTTTGGCCAtttt                                                                                                           >  3:139226/1‑139 (MQ=255)

                             tGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCAttt                                                                                                            >  1:333957/1‑133 (MQ=255)

                             tGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCAttt                                                                                                            <  2:333957/133‑1 (MQ=255)

                               ccATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑g                                                                                                   <  1:178035/139‑1 (MQ=255)

                               ccATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑g                                                                                                   <  2:80767/139‑1 (MQ=255)

                                  tCAATGCCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCt                                                                                                 >  5:215763/1‑138 (MQ=255)

                                    aaTGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGAt                                                                                              >  2:17516/1‑139 (MQ=255)

                                        tCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTa                                                                                           <  4:261426/138‑1 (MQ=255)

                                             ttGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATACAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATaa                                                                                      >  8:172963/1‑138 (MQ=255)

                                                ttttATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATaaaaa                                                                                   >  7:332415/1‑138 (MQ=255)

                                                          tgttgtCAGTTCTTAGACATGTGACATTATATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATGGCGTTTGGGCATTTTTGTCAA‑GCTGATTTACATAAAAAAACAGGCTggg                                                                        >  6:360955/1‑139 (MQ=255)

                                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTcag                                                                    >  4:1510/1‑138 (MQ=255)

                                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTcag                                                                    >  4:172872/1‑138 (MQ=255)

                                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTcag                                                                    >  4:356181/1‑138 (MQ=255)

                                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTcag                                                                    >  8:343905/1‑138 (MQ=255)

                                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTcag                                                                    >  1:85470/1‑138 (MQ=255)

                                                                 atttCTTAGACATGTGACATTAAATTAGCCAAAAGAATA‑TTTTATATACAAACTACAAAAAGTTTCCCTAATGCAAAATTATCGCGTTTGGCAATTTTTGTCAA‑GATGATTTACATAAAAAAACCTGCTCAGTcagcag                                                                 >  8:80416/3‑139 (MQ=255)

                                                                 aGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCTGCTGGGTcagcag                                                                 >  4:7656/1‑139 (MQ=255)

                                                                   ttCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGcc                                                               >  6:259048/1‑139 (MQ=255)

                                                                        aGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTc                                                           >  1:24976/1‑138 (MQ=255)

                                                                        aGACATGTGACAATAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATATTTGTCAA‑GCAGATTTACATAAAAAAACCGGATGGGTCAGCAGCCGCTc                                                           >  1:307458/1‑138 (MQ=255)

                                                                             tgtgACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGTCTGGGTCAGCAGCCGGTCCAAAc                                                      >  3:255967/1‑138 (MQ=255)

                                                                              gtgACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCaacc                                                      >  4:264866/1‑135 (MQ=255)

                                                                               tgACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGTTCAGCAGCCGGTCCaacc                                                      >  1:242365/1‑134 (MQ=255)

                                                                                       aaTTAACCAAAAATATGTTTTTATTAAAACACCAAAAAAATTTACCCACATCAAAAATTATGGC‑TTTGGCCATTTTTGCAAACGTTTATTAAAAAAAAAAACCCGCCTGGGTCACCCGCCGGTCCAAACGAGAAGGGAt                                            <  2:24976/139‑1 (MQ=255)

                                                                                                      tG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACt                            >  2:360008/1‑139 (MQ=255)

                                                                                                       g‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACtt                           >  3:56622/1‑139 (MQ=255)

                                                                                                             atttaCACAGGACAAAAATTTTCCCTCATGCAAAATTATCGCGTTTGGCAATTTTTCTAAA‑GCTTATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTAc                       <  5:161230/138‑1 (MQ=255)

                                                                                                             attaaCACAGCAAAAAAAGTTTCCCTCATCCAAAATTATCGCGTTGGGCCTTTTTTGACAA‑GATAATTAAAAAAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTAc                       <  1:17516/138‑1 (MQ=255)

                                                                                                             aataacacacAACAAAAAGTTCCCCTAATAAAAAATTAGCGCGTTGGGCTATTTTTGACAA‑GCTTATTAAAAAAAAAACACCGGCTGGGGCCGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTAc                       <  7:172963/134‑1 (MQ=255)

                                                                                                                       gACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca             >  7:160241/1‑138 (MQ=255)

                                                                                                                       gACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca             >  4:146305/1‑138 (MQ=255)

                                                                                                                            aaaGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAgtgt       >  6:97930/1‑139 (MQ=255)

                                                                                                                               gTTTCCCTCATGAAAAATTATCGGGTTGGGCCTTTTTTGTCAA‑GCTTATTTAAAAAAAAAACCCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAt    <  7:78767/139‑1 (MQ=255)

                                                                                                                                 ttCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGCGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCtttt  >  5:237081/1‑139 (MQ=255)

                                                                                                                                 ttCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAttt  >  5:218056/1‑139 (MQ=255)

AGCCCTTGTCTCATATTTCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATG‑TTTTATTTACACAGGACAAAAAGTTTCCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAA‑GCTGATTTACATAAAAAAACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCATTT  >  CP006881/2963800‑2964066

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A