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
A3 F1 I1 R1	781	46.9	2231650	93.5%	2086592	109.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,080,915	(G)_5→6	intergenic (+102/‑441)	putP → / → efeU	proline:sodium symporter/ferrous iron permease (pseudogene)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,080,910	1	.	G	100.0%	76.0 / NA	23	intergenic (+97/‑446)	putP/efeU	proline:sodium symporter/ferrous iron permease (pseudogene)
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (15/8); total (15/8)

CTCCGCCGTCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCA‑GGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGATGGACG  >  NC_000913/1080785‑1081043

cTCCGCCGTCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCaa                                                                                                                           >  2:360239/1‑139 (MQ=255)

             gTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGG‑TTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCA‑g                                                                                                                                      >  2:767117/1‑113 (MQ=255)

             gTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGG‑TTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCA‑g                                                                                                                                      <  1:767117/113‑1 (MQ=255)

                        gCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCgccgccgcc                                                                                                                >  2:965135/1‑126 (MQ=255)

                        gCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCgccgccgcc                                                                                                                <  1:965135/126‑1 (MQ=255)

                              ggACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTc                                                                                             >  2:249050/1‑139 (MQ=255)

                                                                                         ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCctg                                                                                                           >  2:1021793/1‑66 (MQ=255)

                                                                                         ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCctg                                                                                                           <  1:1021793/66‑1 (MQ=255)

                                                                                           tCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCg                                                       <  2:932200/116‑1 (MQ=255)

                                                                                           tCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCg                                                       >  1:932200/1‑116 (MQ=255)

                                                                                             gCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGcccc                                                                                                              <  2:695802/59‑1 (MQ=25)

                                                                                             gCCATATAAATTGAATGATGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGcccc                                                                                                              >  1:695802/1‑59 (MQ=21)

                                                                                                           aTGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGccacc                                                               <  2:1072675/92‑1 (MQ=255)

                                                                                                           aTGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGccacc                                                               >  1:1072675/1‑92 (MQ=255)

                                                                                                           aTGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAg                            >  1:787701/1‑127 (MQ=255)

                                                                                                           aTGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAg                            <  2:787701/127‑1 (MQ=255)

                                                                                                            tGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATaa               >  2:738638/1‑139 (MQ=255)

                                                                                                               tGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATcg            >  1:836211/1‑139 (MQ=255)

                                                                                                                        cgcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTg                                                  <  2:277506/92‑1 (MQ=255)

                                                                                                                        cgcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTg                                                  >  1:277506/1‑92 (MQ=255)

                                                                                                                        cgcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGATGGAc   >  2:536609/1‑139 (MQ=255)

                                                                                                                         gcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGa                                                                      >  2:360578/1‑71 (MQ=255)

                                                                                                                         gcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGa                                                                      <  1:360578/71‑1 (MQ=255)

                                                                                                                         gcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGATGGACg  >  2:299060/1‑139 (MQ=255)

                                                                                                                         gcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGATGGACg  >  1:472804/1‑139 (MQ=255)

CTCCGCCGTCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCA‑GGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGATGGACG  >  NC_000913/1080785‑1081043

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