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
A9 F1 I1 R1	64	69.7	3300380	93.4%	3082554	111.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,215,997	A→G	R160R (CGT→CGC)	yehW ←	putative ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,215,997	0	A	G	81.8%	76.5 / 10.2	33	R160R (CGT→CGC)	yehW	putative ABC transporter permease
Reads supporting (aligned to +/- strand): ref base A (2/4); new base G (12/15); total (14/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.27e-01

GCTAAGCCCGATGATGATGGGCGTACCCAGCGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTACGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACGGGCAGCACACCGTAAAGGATCAAGGCGATAATCGCTG  >  NC_000913/2215859‑2216130

gCTAAGCCCGATGATGATGGGCGTACCCAGCGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTa                                                                                                                                       >  1:197861/1‑139 (MQ=255)

  tAAGCCCGATGATGATGGGCGTACCCAGCGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTACg                                                                                                                                     >  2:1037458/1‑139 (MQ=255)

   aaGCCCGATGATGATGGGCGTACCCAGCGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTACGc                                                                                                                                    <  1:1374961/139‑1 (MQ=255)

        cGATGATGATGGGCGTACCCAGCGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCg                                                                                                                               <  2:302141/139‑1 (MQ=255)

                       tACCCAGCGTACTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGCCCTTGCGCACTCGCTGACCACGACTCAt                                                                                                                >  1:1120539/1‑139 (MQ=255)

                        aCCCAGCGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCAtt                                                                                                               >  2:1447391/1‑139 (MQ=255)

                              cGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATa                                                                                                         <  2:945171/139‑1 (MQ=255)

                              cGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATa                                                                                                         >  1:674964/1‑139 (MQ=255)

                                         cTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAAc                                                                                              <  2:68427/139‑1 (MQ=255)

                                                       aTCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCt                                                                                                                             <  1:207691/94‑1 (MQ=255)

                                                       aTCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCt                                                                                                                             >  2:207691/1‑94 (MQ=255)

                                                       aTCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTc                                                                                                                  >  2:270291/1‑105 (MQ=255)

                                                       aTCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTc                                                                                                                  <  1:270291/105‑1 (MQ=255)

                                                        tcgtcgCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTACGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGc                                                                               <  1:1037458/139‑1 (MQ=255)

                                                          gtcgCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTACGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCAt                                                                             <  2:197861/139‑1 (MQ=255)

                                                                  aCCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGa                                                                                                                     <  2:1219284/91‑1 (MQ=255)

                                                                  aCCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGa                                                                                                                     >  1:1219284/1‑91 (MQ=255)

                                                                       tGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAg                                                                <  2:130917/139‑1 (MQ=255)

                                                                            aTAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTgcgc                                                                                                                                    <  1:216939/66‑1 (MQ=255)

                                                                            aTAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTgcgc                                                                                                                                    >  2:216939/1‑66 (MQ=255)

                                                                            aTAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCgg                                                           >  2:571782/1‑139 (MQ=255)

                                                                             tAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCa                                                                                                                        >  1:189251/1‑77 (MQ=255)

                                                                             tAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCa                                                                                                                        <  2:189251/77‑1 (MQ=255)

                                                                             tAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTACGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGc                                                          >  2:1173758/1‑139 (MQ=255)

                                                                                    cGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTc                                                   <  1:571782/139‑1 (MQ=255)

                                                                                      aaGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGc                                                 >  1:861201/1‑139 (MQ=255)

                                                                                           cGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGAc                                                                                                                    >  2:1517693/1‑67 (MQ=255)

                                                                                           cGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGAc                                                                                                                    <  1:1517693/67‑1 (MQ=255)

                                                                                           cGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCa                                            >  2:264195/1‑139 (MQ=255)

                                                                                               cgcccgccAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGAc                                        <  2:1205590/139‑1 (MQ=255)

                                                                                                  ccgccAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACggg                                     <  1:1447391/139‑1 (MQ=255)

                                                                                                       aGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACGGgcagca                                <  1:712178/139‑1 (MQ=255)

                                                                                                              ccGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACGGGCAGCACGCCGTa                         <  1:264195/139‑1 (MQ=255)

                                                                                                              ccGGAGCCGCCAGCGGTAGCTCGACCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACGGGCAGCACACCGTa                         <  2:674964/139‑1 (MQ=255)

                                                                                                                            ggTAGCTCGACCTTACGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACGGGCAGCACACCGTAAAGGATCAAGGCGa           <  1:1173758/139‑1 (MQ=255)

                                                                                                                                     aCCTTGCGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACGGGCAGCACACCGTAAAGGATCAAGGCGATAATCGCTg  >  2:940863/1‑139 (MQ=255)

GCTAAGCCCGATGATGATGGGCGTACCCAGCGTGCTGGCCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAATCACCGGAGCCGCCAGCGGTAGCTCGACCTTACGCACTCGCTGACCACGACTCATTCCCATACCTTTCGCAACTTCTGTCACGCTGGCATCAATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACGGGCAGCACACCGTAAAGGATCAAGGCGATAATCGCTG  >  NC_000913/2215859‑2216130

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A