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
A1 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,427,990	G→A	29.1%	intergenic (+296/‑178)	ydaY → / → ynaA	hypothetical protein/predicted tail protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,427,990	0	G	A	29.1%	123.9 / 60.3	79	intergenic (+296/‑178)	ydaY/ynaA	hypothetical protein/predicted tail protein
Reads supporting (aligned to +/- strand): ref base G (21/35); new base A (7/16); total (28/51)
Fisher's exact test for biased strand distribution p-value = 6.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

TATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATC  >  W3110S.gb/1427926‑1428056

tATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAgt                                                                >  1:1965314/1‑69 (MQ=255)

tATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAgt                                                                >  1:833015/1‑69 (MQ=255)

tATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAgt                                                                >  1:3620353/1‑69 (MQ=255)

tATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAg                                                                 >  1:3179421/1‑68 (MQ=255)

  ttgattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCTCTGGATGACCAGTATTTTCAGGAGCAgtgt                                                              >  1:1157844/1‑69 (MQ=255)

    gattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtg                                                             >  1:2875884/1‑68 (MQ=255)

    gattgaGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtg                                                             >  1:3423746/1‑68 (MQ=255)

             cgATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAgttgtt                                                   <  1:2703057/69‑1 (MQ=255)

             cgATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAgttgtt                                                   <  1:281282/69‑1 (MQ=255)

             cgATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAgttgtt                                                   <  1:3047630/69‑1 (MQ=255)

                tGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAgttgtt                                                   >  1:1525269/1‑66 (MQ=255)

                tGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAAt                                                >  1:2474749/1‑69 (MQ=255)

                tGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAAt                                                >  1:3187516/1‑69 (MQ=255)

                      tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTa                                                  <  1:3302382/61‑1 (MQ=255)

                      tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTa                                                  <  1:2816875/61‑1 (MQ=255)

                      tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTa                                          <  1:2519613/69‑1 (MQ=255)

                      tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTa                                          <  1:3240504/69‑1 (MQ=255)

                      tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTa                                          <  1:336907/69‑1 (MQ=255)

                      tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTa                                          <  1:3401757/69‑1 (MQ=255)

                      tGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAATTACGTa                                          <  1:2855663/69‑1 (MQ=255)

                               gATCTTTGCACTGGATGACCTGTATTTTCAGGAACAGTGTGTGTAgttgtt                                                   <  1:1294754/51‑1 (MQ=255)

                               gATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAgttgtt                                                   <  1:1453169/51‑1 (MQ=255)

                               gATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAgttgtt                                                   <  1:2523275/51‑1 (MQ=255)

                               gATCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAgttgtt                                                   <  1:702815/51‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt                                                          <  1:2147858/43‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt                                                          <  1:292328/43‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt                                                          <  1:2168643/43‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt                                                          <  1:3670292/43‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt                                                          <  1:1079186/43‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt                                                          <  1:2694030/43‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAgtgtgtgt                                                          <  1:2333932/43‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTa                                                         >  1:3257169/1‑44 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAg                                                        >  1:946665/1‑45 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAg                                                        >  1:3531585/1‑45 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTa                                                  <  1:944623/51‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTa                                                  <  1:255182/51‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTa                                                  <  1:9915/51‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTa                                                  <  1:1540787/51‑1 (MQ=255)

                                aTCTTTGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTa                                                  <  1:2232165/51‑1 (MQ=255)

                                   tttGCACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTa                                >  1:226120/1‑66 (MQ=255)

                                       cACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACagag                           <  1:2154409/67‑1 (MQ=255)

                                       cACTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACaga                            <  1:124332/66‑1 (MQ=255)

                                        aCTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAt                         <  1:1485076/68‑1 (MQ=255)

                                        aCTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAt                         <  1:474240/68‑1 (MQ=255)

                                        aCTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAt                         <  1:3616643/68‑1 (MQ=255)

                                        aCTGGATGACCAGTATTTTCAGGAACAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACaga                            <  1:2819273/65‑1 (MQ=255)

                                          tGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgtg                      <  1:2855827/69‑1 (MQ=255)

                                           ggATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTa                                              >  1:1058726/1‑44 (MQ=255)

                                           ggATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTa                                              >  1:3470193/1‑44 (MQ=255)

                                           ggATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTa                                              >  1:2145315/1‑44 (MQ=255)

                                           ggATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTa                                              >  1:3564052/1‑44 (MQ=255)

                                            gATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAt                                                >  1:2271644/1‑41 (MQ=255)

                                            gATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAt                                                >  1:1776507/1‑41 (MQ=255)

                                            gATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAAt                                                >  1:844787/1‑41 (MQ=255)

                                            gATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgt                       <  1:1127346/66‑1 (MQ=255)

                                              tGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGAt                    <  1:1314626/67‑1 (MQ=255)

                                              tGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGAt                    <  1:3403988/67‑1 (MQ=255)

                                              tGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGAt                    <  1:1003135/67‑1 (MQ=255)

                                                     tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGgt                 >  1:972424/1‑63 (MQ=255)

                                                     tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGgt                 >  1:348038/1‑63 (MQ=255)

                                                     tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGgt                 >  1:911389/1‑63 (MQ=255)

                                                     tATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCttt           <  1:1938399/69‑1 (MQ=255)

                                                      aTTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTtta          >  1:312048/1‑69 (MQ=255)

                                                      aTTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTtta          >  1:1235033/1‑69 (MQ=255)

                                                       ttttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTg                                   <  1:2320884/43‑1 (MQ=255)

                                                       ttttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgtg                      >  1:3056971/1‑56 (MQ=255)

                                                       ttttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTtta          >  1:3694952/1‑68 (MQ=255)

                                                       ttttCAGGAACAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCttt           <  1:2125784/67‑1 (MQ=255)

                                                         ttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgt                       <  1:247498/53‑1 (MQ=255)

                                                         ttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgt                       <  1:869318/53‑1 (MQ=255)

                                                         ttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgt                       <  1:3533527/53‑1 (MQ=255)

                                                         ttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGAt                    <  1:2319131/56‑1 (MQ=255)

                                                         ttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGAt                    <  1:1899232/56‑1 (MQ=255)

                                                         ttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGAt                    <  1:2516041/56‑1 (MQ=255)

                                                         ttCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGAt                    <  1:1773971/56‑1 (MQ=255)

                                                           cAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTttaatta      <  1:2005249/68‑1 (MQ=255)

                                                              gAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACaga                            <  1:1241744/43‑1 (MQ=255)

                                                              gAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATc  <  1:871203/69‑1 (MQ=255)

                                                              gAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATc  <  1:2323397/69‑1 (MQ=255)

                                                                gCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgt                       <  1:3087056/46‑1 (MQ=255)

                                                                gCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGAtgt                       >  1:1210068/1‑46 (MQ=255)

TATTGATTGAGCGCGATGAATTTGAAGCAGTGATCTTTGCACTGGATGACCAGTATTTTCAGGAGCAGTGTGTGTAGTTGTTAATTACGTACACTCTGTTACAGAGATGTGATGGTGTCTTTAATTAAATC  >  W3110S.gb/1427926‑1428056

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A