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
A15 F18 I40 R1	11	54.2	1757834	98.4%	1729708	146.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	2,861,917	G→A	Q66* (CAG→TAG)	nlpD ←	activator of AmiC murein hydrolase activity, lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,861,917	0	G	A	95.2%	128.8 / NA	44	Q66* (CAG→TAG)	nlpD	activator of AmiC murein hydrolase activity, lipoprotein
Reads supporting (aligned to +/- strand): ref base G (1/0); major base A (26/14); minor base C (1/1); total (29/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTGCGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACC  >  CP009273/2861781‑2862059

ccATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCGCCGGCTGAATTTGCGGTTGCTGCGCTGTAGGcgt                                                                                                                                    >  1:2138/1‑149 (MQ=255)

 cATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCAGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTAAGCGGTAGGcgtc                                                                                                                                   >  1:391061/1‑149 (MQ=255)

     cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGAcg                                                                                                                                     >  2:570787/1‑143 (MQ=255)

     cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGAcg                                                                                                                                     >  2:272159/1‑143 (MQ=255)

     cTGACGGTTAGAGACGGTGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTcc                                                                                                                               <  1:246804/149‑1 (MQ=255)

                aGACGTTGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTcggc                                                                                                                    <  1:353256/149‑1 (MQ=255)

                aGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTATCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGATTGCTACGCTGTAGACGTCGTCCCCATTTTcggc                                                                                                                    >  1:842825/1‑149 (MQ=255)

                   cGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATGTGTGGCTGCTGCACCGGCTGGATTTGCGGTTGCTACGCGGTAGACGTCGTCCCACTTTTc                                                                                                                       >  2:371862/1‑143 (MQ=255)

                     aTGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTCCGCTGTAGACGTCGTCCCCATTTTcggcggcgg                                                                                                               <  1:589145/149‑1 (MQ=255)

                                 tCCATCTGTACCGGCTTGTTAGCTACTGGCTGCACTGGCTGGATTTGCGGTTTTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTGGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAAt                                                                                                         <  2:188198/143‑1 (MQ=255)

                                   cATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTATGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACAtcc                                                                                                 >  1:443551/1‑147 (MQ=255)

                                     tCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCa                                                                                               <  1:630102/149‑1 (MQ=255)

                                           ccGGCTGCTGAGCTACTGGCTGCACTGGCGGGATTTGCGGTTCCTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATGTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTa                                                                                         <  1:254148/149‑1 (MQ=255)

                                                  ctgAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAg                                                                                        >  2:191259/1‑143 (MQ=255)

                                                  cggAGCTACTGGCTGCACTGGCTGGATTTGCGCTCGTTGAGTAGCCCGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCCTTTTCGGCGGCGGCGTAATCAACACACCAGAATTAg                                                                                        <  2:232849/141‑1 (MQ=255)

                                                       cttcTGGCTGCACTGGCTGGATTTACGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGGATTAGTATTTGCAGgc                                                                             >  1:498896/4‑149 (MQ=255)

                                                       cTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGgc                                                                             >  1:878724/1‑149 (MQ=255)

                                                       cTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATGTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTGATCCACATACCAGAATTAGTATTTGCAGgc                                                                             >  1:498819/1‑149 (MQ=255)

                                                                      nctggTTTTGCGGTTGTTGAGTAGCCTGAANTGGTGGCGGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATGTTCGNCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCa                                                                    <  2:589338/142‑1 (MQ=255)

                                                                      gctggATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCCCCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACg                                                              <  1:44828/149‑1 (MQ=255)

                                                                       ctggATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACgg                                                             >  1:911895/1‑149 (MQ=255)

                                                                        tggATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGa                                                            <  1:768545/149‑1 (MQ=255)

                                                                         ggATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAg                                                           >  1:817379/1‑149 (MQ=255)

                                                                           agttGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCt                                                         <  1:198979/147‑1 (MQ=255)

                                                                           aTTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCt                                                         >  1:51608/1‑149 (MQ=255)

                                                                           aTTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCACCATTTTCGGCGGCGGCGTAATCAACATAGCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCt                                                         >  1:205517/1‑149 (MQ=255)

                                                                            tttGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATGGCCATTCACg                                                              >  2:1730/1‑143 (MQ=255)

                                                                               gCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAg                                                           >  2:111468/1‑143 (MQ=255)

                                                                                cGGCTGTTGATTAGCCAGACTGTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACCTACCCGCATTAGTATTTGCAGGCGCATAGCCCTTAAccgccc                                                          >  2:595262/1‑138 (MQ=255)

                                                                                               cTGAATTTGTGGCTGCTGCTCCGGCTGAATTTGCGGTTGCTTCGCGTTAGCCGCCGACATTTCTGTCGACATCGTCGTGATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGAccggtgccgggg                                           >  2:377851/1‑141 (MQ=255)

                                                                                                   ctttGTGGCTGCTGCACCGGCTGACTTTCCGGCTGCTAAGCTGTTGACGTAGTCCCCATTTTCGGCGGCGGCGTAATCAACCTACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACTGAGCTGACCGGTGCCGGTGGATTTGAAgt                                 <  1:644665/148‑1 (MQ=255)

                                                                                                    tttGTGGGTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGAttt                                      <  2:706218/143‑1 (MQ=255)

                                                                                                    tttGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGGGCTGACCGGTGCCGGTGGATTTGAAgtg                                >  1:234667/1‑149 (MQ=255)

                                                                                                       gtgGCTGCTGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCa                             <  1:301764/149‑1 (MQ=255)

                                                                                                          gctgctGCACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAggg                                >  2:358203/1‑141 (MQ=255)

                                                                                                            tgctgcACCGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGGCGGTGGATTTGAAGTGTCAGAACa                        >  1:849006/1‑149 (MQ=255)

                                                                                                                   ccGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTCATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTCGAAGTGTCAGAACAGCCTgcc                 >  1:533779/1‑149 (MQ=255)

                                                                                                                   ccGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAg                       >  2:267111/1‑143 (MQ=255)

                                                                                                                    cGGCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGc                      >  2:762705/1‑143 (MQ=255)

                                                                                                                     ggCTGAATTTGCGGTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCGGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGcc                     >  2:546210/1‑143 (MQ=255)

                                                                                                                      gCTGAATTTGCGGCTGCTCCGCAGTCGCCGTCTCACGCATTTACGGCGGCGGCGTAATCAACATACCCGAATCAGTATTTGCGGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGGGGGTTTGCAGTGTCAGAACCGCCt                    >  2:381238/1‑143 (MQ=255)

                                                                                                                        tGAATTTGCCGTTGCCACGCTGTAGACGTCCTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTgccagcca            <  1:422829/149‑1 (MQ=255)

                                                                                                                                 ggTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAAc   >  1:97693/1‑149 (MQ=255)

                                                                                                                                  gTTGCTACGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTCACGGAGCTTACCGGTGCCGGTGGATTTGAAGTGTACGGACGGCCTGCCAGCCATAGCGAAAcc  >  1:815316/1‑149 (MQ=255)

CCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGCTGCTGCACCGGCTGAATTTGCGGTTGCTGCGCTGTAGACGTCGTCCCCATTTTCGGCGGCGGCGTAATCAACATACCAGAATTAGTATTTGCAGGCGCATTGCCATTAACGGAGCTGACCGGTGCCGGTGGATTTGAAGTGTCAGAACAGCCTGCCAGCCATAGCGAAACC  >  CP009273/2861781‑2862059

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A