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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,953,026	G→A	71.0%	V361V (GTC→GTT)	pepP ←	proline aminopeptidase P II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,953,026	0	G	A	71.0%	50.3 / 22.8	55	V361V (GTC→GTT)	pepP	proline aminopeptidase P II
Reads supporting (aligned to +/- strand): ref base G (3/13); new base A (12/27); total (15/40)
Fisher's exact test for biased strand distribution p-value = 5.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

ACCATGCCCGGTTCCAGAATGCGCGAGCGATCCTGACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGACGATGGGCGTTCTGAGCGATCAG  >  minE/1952970‑1953094

aCCATGCCCGGTTCCAGAATGCGCGAGCGATCCTGACCATAAACACCCACGTCATGGACATCCAGTCCt                                                          <  1:1825313/69‑1 (MQ=255)

           ttCCAGAATGCGCGAGCGATCCTGACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCt                                               <  1:2720012/69‑1 (MQ=255)

           ttCCAGAATGCGCGAGCGATCCTGACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCt                                               <  1:2819991/69‑1 (MQ=255)

                gAATGCGCGAGCGATCCTGACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGc                                          <  1:3289229/69‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:3130585/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2353903/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2415683/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2455479/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2723597/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2863611/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2902930/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2936452/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:110443/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:3230472/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:444971/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:469322/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:499868/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:510156/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:659020/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:768255/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:933463/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:1430992/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:1347343/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:1177762/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2204999/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:1309713/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:1630512/53‑1 (MQ=255)

                           cgaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:1227694/53‑1 (MQ=255)

                            gaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:3329761/52‑1 (MQ=255)

                            gaTCCTGACCATAAACACCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:214027/52‑1 (MQ=255)

                              tCCTGATCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:437537/1‑39 (MQ=37)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTcc                                                           >  1:1419222/1‑38 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:667395/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:2577899/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:2062719/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:525719/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:2928680/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:131156/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:3085831/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:2330428/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAACGTCATGAACATCCAGTCCt                                                          >  1:35529/1‑39 (MQ=38)

                              tCCTGACCATAAACACCAAAGTCATGAACATCCAGTCCt                                                          >  1:3153358/1‑39 (MQ=25)

                                  gACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGAc                        <  1:714860/69‑1 (MQ=255)

                                  gACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGAc                        <  1:1031935/69‑1 (MQ=255)

                                  gACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGAc                        <  1:983971/69‑1 (MQ=255)

                                  gACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGAc                        <  1:2450630/69‑1 (MQ=255)

                                  gACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGAc                        <  1:1490562/69‑1 (MQ=255)

                                   aCCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCa                                    <  1:1348932/56‑1 (MQ=255)

                                   aCCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCa                                    <  1:2715988/56‑1 (MQ=255)

                                   aCCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCa                                    <  1:1291699/56‑1 (MQ=255)

                                   aCCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCa                                    <  1:1720019/56‑1 (MQ=255)

                                         aaCACCCACGTCATGGACATCCAGTCCTAGCCAGTGGCTAAGGCCATGCATAAAGAAAGGACGATGGGc                 >  1:756845/1‑69 (MQ=255)

                                         aaCACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGACGATGGGc                 >  1:2305649/1‑69 (MQ=255)

                                         aaCACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGACGATGGGc                 >  1:295500/1‑69 (MQ=255)

                                           cacCAACGTCATGAACATCCAGTCCTAACCAGTGGCt                                               <  1:2088515/37‑1 (MQ=38)

                                                        gACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATaaaga                              >  1:3209109/1‑41 (MQ=255)

                                                        gACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATaaaga                              >  1:2220467/1‑41 (MQ=255)

                                                        gACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATaaaga                              >  1:79764/1‑41 (MQ=255)

                                                        gACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATaaaga                              >  1:818532/1‑41 (MQ=255)

                                                        gACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATaaaga                              >  1:2338196/1‑41 (MQ=255)

                                                        gACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGACGATGGGCGTTCTGAGCGATCAg  <  1:1595836/69‑1 (MQ=255)

                                                        gACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGACGATGGGCGTTCTGAGCGATCAg  <  1:3405612/69‑1 (MQ=255)

ACCATGCCCGGTTCCAGAATGCGCGAGCGATCCTGACCATAAACACCCACGTCATGGACATCCAGTCCTAACCAGTGGCTAAGGCCATGCATAAAGAAAGGACGATGGGCGTTCTGAGCGATCAG  >  minE/1952970‑1953094

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

GATK/CNVnator alignment

N/A