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	1,577,907	C→T	39.6%	P10P (CCG→CCA)	xapA ←	purine nucleoside phosphorylase II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,577,907	0	C	T	39.6%	31.9 / 44.0	68	P10P (CCG→CCA)	xapA	purine nucleoside phosphorylase II
Reads supporting (aligned to +/- strand): ref base C (24/17); new base T (9/18); total (33/35)
Fisher's exact test for biased strand distribution p-value = 5.07e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

ATAAAGGCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCTAACGCCTTTT  >  minE/1577845‑1577975

aTAAAGGCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGt                                                                  <  1:2468356/67‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGt                                                                  <  1:675147/61‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:2594049/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:172741/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:1830426/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:2056593/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:2096085/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:2216389/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:2221754/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:248808/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:2433898/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:259967/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:2865268/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:3044591/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:352833/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:449275/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:54273/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:962850/69‑1 (MQ=255)

      gCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:1702406/69‑1 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAAGAGCGGGTTATGAGAAAATTg                                                     >  1:1276208/1‑69 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAAtt                                                      >  1:106172/1‑68 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAAtt                                                      >  1:3107760/1‑68 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTg                                                     >  1:3226250/1‑69 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTg                                                     >  1:3190125/1‑69 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTg                                                     >  1:442403/1‑69 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTg                                                     >  1:462521/1‑69 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTg                                                     >  1:799191/1‑69 (MQ=255)

           tCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTg                                                     >  1:1715939/1‑69 (MQ=255)

            cGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATTCAAAACAGCGGGTTATGAGAAAATTGa                                                    <  1:736637/69‑1 (MQ=255)

               ggCGTGAAAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGaa                                                   <  1:2316559/68‑1 (MQ=255)

               ggCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAAc                                                  >  1:1626320/1‑68 (MQ=255)

               ggCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAAc                                                  >  1:1802059/1‑68 (MQ=255)

                gCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCt                                                <  1:1768510/69‑1 (MQ=255)

                gCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCt                                                <  1:1764521/69‑1 (MQ=255)

                  gTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTga                                              <  1:861769/69‑1 (MQ=255)

                    g‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTgaga                                            <  1:3064244/69‑1 (MQ=255)

                      aaaTCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTgaga                                            <  1:559471/68‑1 (MQ=255)

                        aTCAGGTTTATAAGTCTTGATAATATATATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGaca                                          <  1:2412777/68‑1 (MQ=255)

                         tCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        <  1:3297497/69‑1 (MQ=255)

                         tCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        <  1:2718016/69‑1 (MQ=255)

                         tCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        <  1:1116810/69‑1 (MQ=255)

                         tCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        <  1:849915/69‑1 (MQ=255)

                         tCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        <  1:1717398/69‑1 (MQ=255)

                         tCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        <  1:1878392/69‑1 (MQ=255)

                         tCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        <  1:1520568/69‑1 (MQ=255)

                          cAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        >  1:2614035/1‑68 (MQ=255)

                          cAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        >  1:2527048/1‑68 (MQ=255)

                          cAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        >  1:3057044/1‑68 (MQ=255)

                           aGGTTTATAAGTCTTGATAATATCTACGCAATACAGTGGGTTATGAGaa                                                          <  1:1248341/49‑1 (MQ=255)

                                              atatCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAggg                    >  1:1074943/1‑68 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATacatatat                                     >  1:1904272/1‑50 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATacatatat                                     >  1:2263895/1‑50 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATAcatatata                                    >  1:3011842/1‑51 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATAcatatata                                    >  1:1535885/1‑51 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATAcatatata                                    >  1:2410769/1‑51 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATAcatatata                                    >  1:1712399/1‑51 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATAcatatata                                    >  1:1448237/1‑51 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATAcatatata                                    >  1:1587245/1‑51 (MQ=255)

                                               tatCTACGCAATACAGTGGGTTATGAGAAAACTGAGCCTGATAcatatata                                    >  1:615637/1‑51 (MQ=255)

                                                 tCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        >  1:3097171/1‑45 (MQ=255)

                                                 tCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        >  1:2560810/1‑45 (MQ=255)

                                                 tCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGacata                                        >  1:2942010/1‑45 (MQ=255)

                                                 tCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGa                >  1:1333117/1‑69 (MQ=255)

                                                     tGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCt            >  1:2408695/1‑69 (MQ=255)

                                                       cAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCTaa          >  1:1135216/1‑69 (MQ=255)

                                                       cAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCTaa          >  1:1935356/1‑69 (MQ=255)

                                                       cAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCTaa          >  1:1575435/1‑69 (MQ=255)

                                                       cAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCTaa          >  1:3105313/1‑69 (MQ=255)

                                                               cGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCTAACGCCtttt  <  1:1242700/69‑1 (MQ=255)

                                                               cGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCTAACGCCtttt  <  1:2622848/69‑1 (MQ=255)

ATAAAGGCCACTCGTGGCGTG‑AAATCAGGTTTATAAGTCTTGATAATATCTATGCAAAACAGCGGGTTATGAGAAAATTGAACCTGAGACATACATATCCTTTTTCTGTAGGGTGGAATCTAACGCCTTTT  >  minE/1577845‑1577975

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A